Most people in California receive some of their drinking water supply from the State Water Project (SWP). The SWP also supplies water to over 10% of California’s irrigated agriculture. The SWP and its service area span much of California, delivering water to 29 wholesale contractors shown in Figure 1.
Each year, the Department of Water Resources announces SWP Table A allocations which inform water contractors’ SWP deliveries: “Table A”, “Carryover”, and “Article 21.” What are these different SWP delivery categories and how do they work?
Table A, Carryover, and Article 21 are three types of SWP deliveries described in this post. Some additional, more minor, deliveries are made as: transfer and exchange Table A, and Pool Water deliveries.
The 2020 water year is dry, but the recent May storms led to the increased 2020 SWP Allocation from 15% to 20% of SWP contractors requested “Table A” delivery amounts. Figure 2 compares the initial and final SWP allocations from 1996-2020. Some lessons from this graph include:
2006 was the last 100% allocation year, 14 years ago.
Final allocations usually increase significantly from the initial allocation estimate, usually sent to SWP contractors by end of October. However, final allocations could be less than initial allocation estimates in extreme dry years.
Drought years tend to have little or no increases from initial to final SWP allocations (such as 2007-2009 and 2012-2015).
It is likely that 2020’s final allocation will be 20%. The last 20% final allocation year was in 2015, one of the driest years on record.
Figure 3 shows Table A, Carryover, and Article 21 deliveries from 2000-2017. Minimum, average, and Maximum Table A and carryover statistics were combined because both are categorized under Table A water while Article 21 deliveries are made above the approved Table A amounts. 2014 had the least Table A and carryover deliveries at 475 TAF while 2003 contained the most at 3202 TAF.
Figure 3: Historical SWP Deliveries (TAF) by category from 2000-2017 (Data from CA DWR 2009, 2012, and 2018).
What is Table A?
Table A allocations represent “a portion or all of the annual Table A amount requested by SWP water contractors and approved for delivery by DWR (CA DWR 2019).” DWR and the public water agencies and local water districts developed the SWP’s long-term water supply contracts in the 1960s. Table A contract amounts originated from these long-term contracts and have been amended. The 1994 Monterey Agreements significantly revised the long-term water supply contracts. Table 1 presents each contractor’s maximum Table A contract delivery amount, adding up to 4.17 million AF, anticipated to be the SWP’s ultimate delivery capability in the 1960s (an amount rarely actually available). As a wet year example, the last column indicates how much each water contractor utilized their Max Table A amount in 2006, a 100% allocation year. San Joaquin contractors were more likely to take their full Table A and supplement water supplies with Article 21 water, described later.
Table 1: Share of total Maximum Table A amount (4.17 MAF) between all 29 SWP Contractors at Calendar Year 2020(CA DWR 2019) and % Utilization of Table A deliveries at 100% Allocation year in 2006(CA DWR 2015). Largest Table A contract holders and highest 100% allocation utilizers highlighted. 2006 total deliveries also include turnback pool water.
What is Carryover water?
Carryover water is a portion of Table A water that contractors may save for next year’s delivery. Carryover requests allow SWP contractors to store some of their annual allocation for the next year, and not lose undelivered allocation at the end of the SWP contract year, December 31. When contractors request carryover for next year’s delivery, that water is stored in the SWP’s share of San Luis reservoir in Merced County.
However, storing carryover water in San Luis reservoir has a low operating priority and so brings a risk. SWP contractors can lose this stored carryover water when San Luis Reservoir fills. In the 2017 wet year, some contractors (Santa Barbara County , Crestline Lake Arrowhead Water Agency and San Gorgonio Pass Water Agency) needed to transfer their carryover water from San Luis to another non-SWP facility to prevent losing their carryover storage. Figure 4 shows how San Luis filled in 2017 for the first time since 2011, following the 2012-2016 drought.
Figure 4: San Luis reservoir levels (TAF) from January 2000 to April 2020 with wettest and driest water year designations using the Sacramento Valley Index (CA DWR 2020a; c).
Overall, San Luis carryover water provides water contractors with a safety net in dry years, like 2020. During the 2012-2016 drought, contractors almost exclusively relied on only Table A and carryover. 2014 was the only year when carryover deliveries (383 TAF) exceeded those of Table A (92 TAF) (Figure 3). Carryover storage acts as a “savings bank account” which water agencies can draw on in dry conditions, but at some risk in very wet years.
What is Article 21 water?
Article 21 (described in water contracts) allows water contractors to take deliveries above approved and scheduled Table A amounts (CA DWR 2019). Article 21 is sometimes called interruptible, unscheduled, or surplus water. It is offered predominantly in wet years (2005, 2006, 2011, and 2017) (Figure 5).
Article 21 deliveries do not interfere with SWP allocations.
Excess water is available in the Delta.
Conveyance is not being used for SWP purposes or scheduled SWP deliveries.
Article 21 water may not become Carryover water, stored in SWP facilities.
The different types of SWP deliveries are akin to managing household finances. Table A deliveries are like a monthly paycheck for fixed recurring expenses. Carryover requests let you save part of your “Table A paycheck” for the future. Lastly, Article 21 deliveries are like an unusual annual bonus. You could splurge your “Article 21 water” bonus for direct retail delivery, or save it in an aquifer or reservoir outside the SWP.
In California’s highly variable climate, each water contractor must match these SWP water supplies, other local and regional water resources, and water demands for this year’s water use and in preparing for future droughts. In this dry 2020 year, SWP contractors are likely aware that the next drought could be just around the corner.
Nicole Osorio is a first year Master’s student of Water Resources Civil Engineering at the University of California, Davis.
Foothill Yellow-legged Frogs have begun to spawn, laying small snow-globe sized egg masses in streams and rivers. They are one of the few stream-breeding frogs endemic to California and Oregon. This species is a good indicator of stream health because they link aquatic and terrestrial ecosystems and are strongly tied to natural seasonal cues associated with local hydrology. Historically, they occurred in streams and rivers throughout California and Oregon, but, as with many amphibians, they have precipitously declined in many parts of their range due to river regulation, habitat loss, and disease.
First petitioned for listing under the California Endangered Species Act (CESA) in 2016 by the Center for Biological Diversity, the California Fish and Game Commission recently listed Foothill Yellow-legged Frogs (Rana boylii) in February 2020. But unlike other species listed under CESA, Foothill Yellow-legged Frogs are one of the first species where genetic data were used to introduce more nuance into the regulatory process. Only a few other species have used a genetic basis to identify groups for listing under the CESA. For example, Coho Salmon Oncorhynchus kisutch (listed in 1995) used a single status listing for the species based on existing genetic data. Similarly, the Fisher (Pekania pennanti) was also listed/not listed using evolutionarily significant units (ESUs), but the species is extremely geographically separated, unlike the historically wide-ranging Foothill Yellow-legged Frog. For Foothill Yellow-legged Frogs, different genetically distinct groups were given different listing status (Threatened, Endangered, or listing not warranted at this time). This listing is not an endpoint, it reflects successful collaboration between researchers and regulators to provide a pathway to better prioritize long-term management and conservation of one of California’s iconic species.
While protecting and conserving one of our few native frog species is important, using the same uniform listing and management strategy for every frog population in California may not be practical. The Foothill Yellow-legged Frog has a large range that historically encompassed most of California, thus a blanket approach to listing and conservation management across the state may not be very effective. Different regions of the state have different impacts on the species; therefore it makes sense and is likely more effective and cost-efficient to manage conservation at a regional scale. A more nuanced approach also avoids placing a regulatory burden on entities in areas where the species appears to be doing well. Finding options to build more flexibility into the system we use to manage and conserve our natural resources is important for long-term success. The crux of this success is best illustrated by a deceptively straightforward map (Figure 2). Despite its simplicity, this map is a result of several years of genetic research and collaboration between multiple agencies and universities. Its use in the state listing process is a relatively novel application of conservation genetics.
Ultimately the boundaries on this map provide a flexible but robust way to prioritize each clade or genetic group independently. Because each group is genetically distinct, the map allows us to describe each group using metrics that include genetic diversity as well as landscape change and flow alteration. Measuring genetic diversity within and among each of these groups is important because genetic diversity provides a species with the ability to adapt to changing conditions (i.e., evolve). A loss of diversity often signals extreme population and range reductions, and is associated with a loss of fitness (reproductive success and survival). Genetic data enables us to quantify which groups had more or less genetic diversity, and this was combined with regional information about the impacts of flow regulation, habitat alteration, and disease, to identify which groups may be most at risk of extinction. This allowed the CDFW to identify, prioritize, and list each clade separately, and make clade-specific listing recommendations, which provided a much more practical way to evaluate and apply CESA in a historically wide-ranging species (CDFW 2020).
And importantly, there was consensus in these findings; a separate independent study conducted at UCLA found a strikingly similar pattern, lending additional support to these genetic boundaries (McCartney-Melstad et al. 2018). The boundaries on this map can be updated, and these data provide additional benchmarks that give us insight into the status and health of different populations which can be compared across time and location. Translating the information that DNA provides us provides a powerful tool to help bridge the need for “the best available science” in conservation, but ultimately the most effective tools rely on our ability to collaborate and communicate across boundaries.
The map shows the genetic boundaries for distinct interbreeding populations, called clades, for the Foothill Yellow-legged Frog. This map helped define how and where the Foothill Yellow-legged Frog would be listed under CESA, and it provides a unique and powerful way to use DNA as a way to inform conservation.
Drawing boundaries with DNA is not new. Delineating geographic ranges for organisms based on their underlying genetic code has been one of the foundational components of population genetics, but integrating this information into legal conservation frameworks like the state and federal Endangered Species Acts has been a slow process. The Endangered Species Act requires decisions be based on the “best available science.” While this sounds like a decision that would be heavily based on quantifiable data, it requires judgement and interpretation to incorporate the full spectrum of biological data when classifying a species as Endangered, Threatened, or listing not warranted. With the advent of modern genetics, the types of data that can be used can be powerful and informative, but also complicated and very dense. So how do we use genetic tools and translate this information into defensible policy and legal conclusions?
In an era where we can generate more data than ever before, where specializations abound, and the competition to maintain funding to conduct research has greatly emphasized novelty, the ability to translate across disciplines and find ways to effectively apply science may seem rare. Ultimately, there is a continuum between research and management, and from a management perspective, the best information is actionable, discrete, and can be integrated into existing policy frameworks. For scientists interested in applied research, this means understanding the context where the research may be used, identifying what gaps exist within a given framework, and actually talking with the folks who will use the science.
When I started my dissertation, I tried to think critically about what would be useful for management. I spent time talking to resource managers at state and federal agencies, and I tried to maintain communication and collaborations throughout the process. In particular, I tried to ask what pieces of information or research would be critical for helping inform conservation of the species. Maps are crucial for identifying, prioritizing, and planning, so identifying and refining boundaries for conservation units (distinct populations, or clades) was an important component in the listing process. In the end, some key pieces of my dissertation were used in the Status Review used for the California Department of Fish & Wildlife (CDFW) listing recommendations for the Foothill Yellow-legged Frog (CDFW 2019). While it is bittersweet to work with a species that is at risk of extinction, it is encouraging to participate and contribute in a meaningful way to a conservation process as a scientist.
Ryan Peek is a post-doctoral researcher at the Center for Watershed Sciences, UC Davis.
McCartney-Melstad, E., Gidiş, M., & Shaffer, H. B. (2018). Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining Foothill Yellow-legged Frog. Heredity, 121(2), 112–125.
Peek, R.A. (2018). Population Genetics of a Sentinel Stream-breeding Frog (Rana boylii) [Ecology]. PhD Dissertation. University of California, Davis.
Laura Patterson has been instrumental as an contributor and collaborator; she coordinated and prepared the status review report for CDFW. In addition, Brad Shaffer, Sarah Kupferberg, Amy Lind, Sarah Yarnell, and Jennifer Dever have all provided data and critical research towards conservation of this species.
by Alvar Escriva-Bou, Jay Lund, Josue Medellin-Azuara, and Thomas Harter
Earlier this year, the first local Groundwater Sustainability Plans (GSPs) were submitted to California’s Department of Water Resources for basins with the most severe groundwater overdraft. To comply with the Sustainable Groundwater Management Act, these plans must address any “significant and unreasonable” impacts of groundwater overdraft that occurred after January 1, 2015, including lowering groundwater levels and other “undesirable results.” The math for ending overdraft is simple: groundwater basins must balance their budgets, by increasing groundwater recharge and reducing pumping.
In principle, evaluating the adequacy of these plans to achieve sustainability should also be simple: Does the anticipated reduction in pumping plus increase in recharge equal or exceed the basin’s long-term rate of overdraft?
In practice, however, it’s not so simple. Water supply in California is dynamic and variable, and groundwater overdraft can vary widely from year to year. In dry years more groundwater is pumped to replace reductions in surface water deliveries, while in wet years more water is recharged. Cropping patterns also vary annually with market conditions, agronomic conditions (fallowing, salinity, etc.), and labor availability, all of which can affect regional water use. Even estimates of long-term average overdraft have considerable uncertainty, due to California’s hydrologic variability and uncertainties in data and models used to estimate water balances. For instance, model estimates of average statewide groundwater overdraft for different periods range from 1.4 to 9.1 million acre-feet (maf) per year (Brush et al., 2013; Escriva-Bou, 2019; Famiglietti et al., 2011; Faunt et al., 2009; Xiao et al., 2017). Considering all these uncertainties, plans based on rigid and static assumptions are bound to miss their targets.
So how do we know if a proposed Groundwater Sustainability Plan will succeed? Or, put another way, how can we plan for sustainability given all these uncertainties?
Although we can’t ever be sure, we can make reasonable estimates that account for the range of uncertainties. In a recent paper, we outline a method for estimating the likelihood of achieving groundwater sustainability. This method highlights the relationship between restrictions on groundwater pumping and the likelihood of maintaining groundwater levels, trade-offs between pumping restrictions and agricultural revenue losses, and implications of defining thresholds—such as minimum groundwater levels—as part of sustainability plan rules.
Our analysis highlights the dynamic character of hydrology and water use in California’s Central Valley. Although we illustrate the method using regional modeling estimates of overdraft and hydrology that were available prior to the release of the new GSPs, the analysis is relevant for groundwater sustainability agencies as they implement and refine their plans going forward. The method can be applied to help estimate uncertainties in these plans, reduce these uncertainties over time, and plan adaptively for sustainability, considering the economic consequences of varying pumping restrictions and thresholds.
Here we highlight some of the paper’s main lessons.
Greater pumping restrictions increase the likelihood of ending overdraft
Uncertainty in overdraft arises from the state’s highly variable climate, uncertainties in future water use decisions, and imperfections in models and data representing water balances.
We estimated uncertainty in annual overdraft for 21 Central Valley sub-regions using the results of recent hydrologic history (1975-2003) of two Central Valley groundwater models (USGS’ CVHM and DWR’s C2VSIM). Each model’s results show variability in annual water balances and overdraft. The differences between these models’ results can represent the uncertainty of data and models.
Our analysis directly combines both sources of uncertainty. A simple approach is to estimate average annual overdraft as the average of model results, and estimate the variability of annual overdraft from the standard deviation of these results. A simple statistical equation can be used to estimate the probability of accumulated future overdraft for a given net reduction in pumping over a specified number of years. By defining sustainability as the inter-annual fluctuation of the groundwater table that does not exceed a minimum threshold (Figure 1), it is possible to estimate the probability of achieving sustainability as a function of the net reduction in groundwater use.
Figure 1: Hypothetical representation of changes of groundwater storage over time and definition of minimum thresholds to define sustainability
Figure 2 shows results for all 21 Central Valley sub-regions. A net reduction in water use equaling the average level of overdraft has a 50% chance of achieving sustainability in any time period. Greater reductions in net water use increase the probability of ending overdraft, although the rates (the slope of the curves) vary across sub-regions depending on local conditions. For example:
Sub-regions that are sustainable (but that could become unsustainable with unfavorable conditions). Sub-regions 9 (Delta) and 12 (Turlock Basin) are sustainable on average, with positive average annual change in groundwater storage. Without net water use reductions their chances of balancing groundwater levels in 20 years exceed 70%, but with unfavorable hydrologic conditions they would have to reduce net water use to ensure sustainability.
Sub-regions with low levels of unsustainable pumping. Sub-regions 10 (Delta-Mendota Basin) and 11 (Modesto and southeast San Joaquin Basin) have some average annual overdraft (< 10 taf/year). Without net water use reduction, they would have almost a 50% chance achieving sustainability over next 20 years. To ensure sustainability for any future hydro-climatic conditions, they would have to reduce water use by much more (~ 80 taf/year).
Sub-regions with large values of unsustainable pumping. Sub-regions 8 (the valley floor east of the Delta) and 13 (Merced, Chowchilla, and Madera Basins) have larger average annual overdraft (55 and 116 taf/year respectively). Their larger variances also make the curves flatter. These sub-regions still have a 20% chance of becoming sustainable without reducing water use. Net use reductions at least three times the current level of overdraft are needed to reliably achieve sustainability.
For longer regulatory horizons, the range of pumping reductions for different probabilities narrows around the estimated average annual overdraft because the statistical average becomes more likely to dominate over rare favorable or unfavorable hydrology over longer periods.
Two caveats are worth mentioning. First, this analysis assumes all overdraft is addressed by net reductions in groundwater use. Smaller reductions will be needed if groundwater recharge can be increased in wet seasons and years. Some estimates find that 15-30% of long-term overdraft in the Central Valley could be supplied by additional groundwater replenishment (DWR 2018; Kocis and Dahlke 2017, Escriva-Bou and Hanak 2018). This could significantly reduce the economic impact of pumping restrictions. Second, our results are based on DWR’s C2VSim and USGS’s CVHM models, developed for the Central Valley. These models may have some difficulties representing local groundwater basins—the relevant geographic focus for GSPs. Even if GSPs are able to incorporate more accurate local estimates of overdraft and historic hydrology, it will still be important for these plans to estimate the uncertainties of these and other parameters in evaluating the likelihood of attaining groundwater sustainability.
Figure 2. Probability of ending groundwater overdraft in year 2040 for a range of net groundwater pumping reductions for all Central Valley sub-regions
Increasing the likelihood of achieving sustainability rapidly raises agricultural economic losses
We also estimated economic costs and probabilities of achieving sustainability over different periods. Here, we assumed the sub-regions achieve sustainability only by reducing agricultural water use, with internal water markets within each sub-region.
Trade-off curves of the reliability of achieving sustainability versus economic costs of reducing farm water use follow an S curve (Figure 3). Small water use reductions have low likelihood of achieving sustainability, and lower economic costs for agriculture. Achieving sustainable groundwater levels with higher reliability requires more pumping reductions and much higher economic costs, because this requires curtailing water for more valuable crops. For example, the average cost to achieve a 50% chance of groundwater sustainability in sub-region 15 over 20 years is $10 million/year. However, to achieve nearly 100% reliability of sustainability would cost roughly six times more in lost crop revenues. Much longer compliance horizons lessen the tradeoff between farm sector costs and reliability of attaining sustainability.
Figure 3: Higher likelihood of achieving groundwater sustainability reduces farm revenues (example for sub-region 15)
An important caveat is that we only account for agricultural revenue losses from reducing overdraft in this study. Plans would also need to consider costs of not reducing overdraft, including infrastructure damage related to land subsidence, capital costs of stranded wells, higher pumping costs, dry drinking water wells, and harm to groundwater-dependent ecosystems.
Initial overdraft estimates will almost certainly be wrong. Uncertainties in data and models should be considered when developing overdraft estimates for Groundwater Sustainability Plans, and the plans should provide ranges of estimates. For instance, overdraft estimates for different historical periods could show the potential range of hydrologic variability, and the implications of this variability for attaining sustainability.
Groundwater pumping restrictions will need to vary across years. To accommodate future droughts within the compliance horizon for attaining sustainability, required reductions in water use will need to vary across years. Groundwater demand is generally higher during droughts, when less surface water is available. As droughts progress and groundwater is drawn down, pumping shares should be adjusted to avoid reaching the minimum threshold for groundwater levels too early, potentially causing significant investment losses in perennial crops.
Long-term pumping and recharge efforts will likely need to adjust over time. Anticipating and building such adjustments into local groundwater plans should make it easier to implement plans and to anticipate changes in groundwater availability, as well as make it easier for state agencies to evaluate plans.
Successful groundwater sustainability plans and institutions will analyze uncertainty to prepare to adapt to variable hydrology and new estimates of overdraft. Adaptive methods to account for California’s hydrologic variability and the inherent uncertainties are essential for a dynamic response to changing conditions. SGMA’s requirement that GSPs update their plans at least every five years provides an important opportunity to incorporate new information and lessons, and adapt to changing conditions.
State regulators can help by providing common regional templates, data, and models for analysis and institutional response. To facilitate the transition to stronger sustainability accounting—incorporating uncertainties—state technical assistance should focus on standardizing and improving the quality of the data, documentation, modeling, and other key tools for GSP planning and implementation. DWR’s Draft Handbook for Water Budget Development (2020) may be a step in this direction.
Brush, C.F., Dogrul, E.C., Kadir, T.N., 2013. Development and Calibration of the California Central Valley Groundwater-Surface Water Simulation Model (C2VSim), Version 3.02-CG. California Department of Water Resources, Bay-Delta Office.
DWR (California Department of Water Resources) 2018 Water Available for Replenishment Report (Sacramento CA: California Department of Water Resources) (Now seemingly unavailable from the DWR website)
Famiglietti J S, Lo M, Ho S L, Bethune J, Anderson K J, Syed T H, Swenson S C, de Linage C R and Rodell M 2011, “Satellites measure recent rates of groundwater depletion in California’s Central Valley,” Geophy. Res. Lett.38
Kocis, T.N. and H.E.Dahlke, 2017. Availability of high-magnitude streamflow for groundwater banking in the Central Valley, California. Environmental Research Letters. https://doi.org/10.1088/1748-9326/aa7b1b
Scanlon B R, Faunt C C, Longuevergne L, Reedy R C, Alley W M, McGuire V L and McMahon P B 2012 Groundwater depletion and sustainability of irrigation in the US high plains and central valley Proc. Natl Acad. Sci. 109 9320–25
Xiao M, Koppa A, Mekonnen Z, Pagán B R, Zhan S, Cao Q, Aierken A, Lee H and Lettenmaier D P 2017 How much groundwater did California’s Central Valley lose during the 2012–2016 drought? Geophy. Res. Lett. 44 1–8
Alvar Escriva-Bou is a Research Fellow with the Public Policy Institute of California. Jay Lund is the Director of the Center for Watershed Sciences and a Professor of Civil and Environmental Engineering at the University of California, Davis. Josue Medellin-Azuara is an Associate Professor of Environmental Engineering at the University of California, Merced. Thomas Harter is a Professor of Hydrology and Cooperative Extension Specialist at the University of California, Davis.
“Nowhere is the biodiversity crisis more acute than in freshwater ecosystems” (Tickner et al. 2020)
Weeks of being confined indoors under shelter-in-place orders increases our appreciation of the natural world. Walking and exercising outdoors, especially along a local stream like Putah Creek, is one of the best ways to escape the news cycle and to restore a sense of well-being. Quiet streets and pathways have invited a growing chorus of bird song and can even inspire interest in watching hatches of mayflies rising off gurgling stream waters. Online livestreaming of wildlife cameras has surged. These experiences remind us how California’s natural environments and rich biological diversity improve the quality of our lives. They also remind us that this natural heritage is threatened. California harbors more unique plants and animals than other state in the U.S but an estimated 30 percent of our native species are now threatened with extinction (Mooney and Zavaleta 2016).
Sustaining the amazing diversity of life on this planet and in California in particular is a major challenge of this frenetic era. The importance of this protection is reflected in the growing realization that maintaining the diversity of native species living in healthy ecosystems also results in an environment that is good for people. However, the demand of California’s ever-increasing citizenry for intensive use of our land and water makes this challenge extremely hard to meet. Meeting the challenge has just been made even more urgent by the new finding that since 2000 California and the western USA has been experiencing a megadrought, in part because of the aggravations of climate change. This era is being pegged as the driest period in over 500 years and there is no reason to think it is not going to continue, despite occasional wet years.
A major response to the state’s biodiversity challenge by the state has been the California Biodiversity Initiative of 2018, which was supported by Governor Brown and continues to be supported by Governor Newsome. The initiative proposes statewide measures to halt the decline of native species and ecosystems, under the leadership of the Department of Fish and Wildlife and the Department of Food and Agriculture.
We applaud this initiative as a good beginning, even if stalled by the effects of the present pandemic. However, it also has a major flaw: it is so focused on terrestrial ecosystems and native plants that it overlooks the needs of native aquatic (freshwater) species, habitats, and ecosystems. California’s aquatic biodiversity is particularly imperiled, as it is worldwide (Tickner et al. 2020). This problem is most clearly reflected in status of our native fishes. Of our 125+ native fishes, seven species are already extinct and 100 species are in decline and may be ultimately threatened with extinction. These include 31 species already listed as Threatened or Endangered under the state and federal Endangered Species Acts and 62 species listed as Species of Special Concern by CDFW (Moyle et al. 2011, 2015). These species include salmon and steelhead that are both iconic and support valuable fisheries.
Native fish declines are mirrored by other freshwater taxa. Howard et al. (2015) conducted the first statewide status assessment of California’s freshwater taxa. They found that of about 2,000 freshwater vascular plants, macroinvertebrates, and vertebrates for which adequate information was available, half were ranked as vulnerable (data were lacking for the other ~2,000 freshwater taxa in the state). California’s vulnerable aquatic organisms were mostly endemic species, found nowhere else in the world. But among the vulnerable taxa, only 113 (6%) were listed as endangered or threatened under the federal or state ESAs indicating a general neglect of non-charismatic species.
California has taken notable steps to protect its biodiversity, primarily through the establishment of protected lands under various programs. Unfortunately, efforts to protect terrestrial habitats and ecosystems rarely do an adequate job of protecting aquatic biodiversity; most of the key rivers that support threatened fishes, for example, flow outside of protected areas (Grantham et al. 2016). Of course, because terrestrial ecosystems drain into or encompass freshwater systems, management of terrestrial habitats is important for conserving aquatic habitats. However, most protected areas in the state are not explicitly managed to maintain freshwater ecosystems and their biota.
If native freshwater biodiversity is to be conserved, a systematic, statewide approach is required. Building on previous work by Howard et al. (2018), Grantham et al. (2016), Moyle (2002) and Moyle and Yoshiyama (1996), we argue that such an approach should be centered on the designation of priority watersheds and/or habitats for freshwater species management. Moyle (2002) identified a network of streams, lakes, spring systems, wetlands, and watersheds throughout the state that could potentially support all of the state’s native freshwater fishes and include representative examples of all of California’s aquatic habitats (as described by Moyle and Ellison 1991). Grantham et al. (2016) and Howard et al. (2018) extended this approach by using systematic conservation planning methods (Linke et al. 2011) to identify a network of watersheds in California that most efficiently encompass the distribution of all native freshwater taxa. Collectively, these studies provide an ecosystem-based blueprint for pursuing a systematic, statewide approach to freshwater biodiversity conservation, through Freshwater Protected Areas (FPAs), inspired by California’s system of Marine Protected Areas (MPAs).
In addition to the designation of FPAs, water supplies must also be secured for aquatic biodiversity protection. All aquatic species depend upon a sufficient quantity and quality of water throughout the year, no matter what type of habitat they live in. This is particularly true of riverine species that have adapted to the natural variation in seasonal flows – including winter high flows and summer low flows – that characterize the state’s rivers and streams. Yet most of California’s flowing waters have been dammed, diverted, and otherwise modified (Grantham et al. 2014), activities which have altered natural flow patterns and impaired aquatic habitats (Zimmerman et al. 2018). Only a small proportion of the state’s rivers and streams have environmental flow protections and many of these are managed mainly for single species, such as ESA-listed salmon and steelhead. Recently, a working group of researchers and agency staff has been developing a California Environmental Flows Framework (Obester et al. 2020; ceff.ucdavis.edu). The Framework includes technical tools and guidance for developing environmental flow standards in streams throughout the state, focusing on specific functional elements of the flow regime linked to ecosystem health (i.e., functional flows). The overall goal of the Framework is to support a more consistent, and comprehensive approach to managing water for the environment in California.
The protection of California’s aquatic biodiversity, incorporating the above approaches, will require a large-scale effort. This effort should start now and accelerate when people and conservation agencies are less distracted by the effects of the COVID-19 epidemic, including a distressed economy. We can envision actions to protect aquatic biodiversity as being part of the economic recovery efforts for California.
Priority actions include:
1. Update and invest in mapping and assessment of freshwater taxa and habitats.
One reason that the state has been unable to implement a systematic strategy for managing native freshwater biodiversity is the limited collection, poor organization, and inaccessibility of data. Several recent efforts, including the PISCES database for tracking of the distribution of native fishes (Santos et al. 2013) and the California Freshwater Species Database for tracking additional freshwater species (TNC 2015), have been difficult to update and sustain because of lack of funds and personnel. Other data sources are either inaccessible to the public (e.g, California Natural Diversity Data Base) or are poorly organized (e.g., Biogeographic information and Observation System [BIOS]). These should be vetted, reorganized, and published, following modern data management and open source principles. TNC’s California State of Salmon website attempts to provide accessible data for all watersheds with salmon and steelhead monitoring (https://casalmon.org/). However, monitoring programs are inadequate for accurately tracking the status of even these iconic species. Most other species are either monitored opportunistically or not at all. Successful management of the state’s freshwater biota and ecosystems cannot be achieved without a robust, comprehensive monitoring program.
2. Designate and manage Freshwater Protected Areas (FPAs).
We already have a good idea where many of the most important areas for freshwater species conservation are located. However, there has been no formal designation or concentrated effort to identify and prioritize such areas for conservation and management actions. The 2018 Biodiversity Initiative aims to protect 20 percent of each major ecosystem type in the state, including freshwater ecosystems and to restore 15 percent of each ecosystem type from its degraded status. While this sounds good, the numbers are arbitrary and reflect terrestrial thinking. For rivers, for example, how do you protect an ”ecosystem type” that has not been clearly defined and changes as it flows downstream? Does it mean establishment of a statewide network of watersheds focused on their restoration and protection? If that is the case, how big (hydrologic unit) should each watershed in the system be? Whatever the units, FPAs should provide habitat for as much of the native aquatic biota as possible, throughout the state. Previous work by Moyle (2002), Grantham et al. (2016), and Howard et al. (2018) establish a blueprint for delineating FPAs that could efficiently protect native freshwater biodiversity and habitats. With this information, a team of scientists, such that assembled for the California Biodiversity Initiative, should be able to come up with a site-specific plan to implement an FPA strategy, if California is willing to support it. The plan would, based on both expert opinion and computer algorithms, could provide preliminary designations of potential FPAs, much as Moyle and Randall (1998) did for Sierra Nevada watersheds. These could then be investigated more closely and appropriate action taken to protect the most imperiled FPAs.
3. Accelerate implementation of environmental flows.
California Environmental Flows Framework provides guidance for developing flow recommendations to maintain healthy freshwater ecosystems. The Framework provides a set of flow criteria (based on predictions of functional flows informed by reference stream hydrology) that can be used to immediately establish environmental flow standards in rivers where they do not exist. In rivers and streams with existing flow protections, the Framework can be applied to refine standards so that they are more effective in supporting ecosystem health. On-the-ground pilot projects are needed to implement the Framework across the diversity of California’s rivers and management contexts. As the foundation of the Framework, the functional flows approach also recognizes that environmental flow protections be coupled with strategic investments in physical habitat improvements, such as levee setbacks and barrier removals. For large rivers, it is particularly important to restore their connectivity to their floodplains to support the biological and physical functions that sustain salmon and other native species.
In short, California does a poor job of protecting aquatic biodiversity. A bold and imaginative, systematic effort is needed to protect and manage aquatic biodiversity. This will take leadership, money, and dedication to getting the job done by federal, state, and local agencies. As a biodiversity hotspot with an economy bigger than most nations, California should be leading the country and the world in protecting its aquatic systems. We have the tools at hand, but have been unable to muster the will to do the hard work. But as we reflect upon the natural world during the current public health crisis, it just may be that our growing appreciation of California’s biological richness is what is needed to inspire meaningful action.
Peter Moyle is an emeritus professor at the Center for Watershed Sciences, UC Davis. Jeanette Howard leads The Nature Conservancy’s freshwater science team for California; Ted Grantham is a Co-operative Extension Specialist in the Department of Science, Policy, and Management, UC Berkeley.
Grantham, T.E., J. H. Viers, and P.B. Moyle. 2014 Systematic screening of dams for environmental flow assessment and implementation. Bioscience 64: 1006-1018.
Grantham, T. E., K.A. Fesenmyer, R. Peek, E. Holmes, R. M. Quiñones, A. Bell, N. Santos, J.K. Howard, J.H. Viers, and P.B. Moyle. 2016. Missing the boat on freshwater fish conservation in California. Conservation Letters. DOI: 10.1111/conl.12249.
Howard J.K. and 20 others. 2015. Patterns of freshwater species richness, endemism, and vulnerability in California. PLoS ONE 10(7): e0130710. doi:10.1371/journal.pone.0130710.
Howard, J.K. and 10 others. A freshwater conservation blueprint for California: prioritizing watersheds for freshwater biodiversity. Freshwater Science 37(2): 417-431.
Linke, S., E. Turak, and J. Nel. 2011. Freshwater conservation planning: the case for systematic approaches. Freshwater Biology 56(1): 6-20.
Mooney, H. and E. Zavaleta. Ecosystems of California. Berkeley: University of California Press, 2016.
Mount, J., B. Gray, K. Bork, J. E. Cloern, F. W. Davis, T. Grantham, L. Grenier, J. Harder, Y. Kuwayama, P. Moyle, M. W. Schwartz, A.Whipple, and S.Yarnell. 2019. A Path Forward for California’s Freshwater Ecosystems. San Francisco: Public Policy Institute of California. 32 pp.
Moyle, P. B. 2002. Inland Fishes of California: Revised and Expanded. Berkeley: University of California Press.
Moyle, P. B., and J. Ellison. 1991. A conservation-oriented classification system for California’s inland waters. California Fish and Game 77:161-180.
Moyle, P.B., J. V. E. Katz and R. M. Quiñones. 2011. Rapid decline of California’s native inland fishes: a status assessment. Biological Conservation 144: 2414-2423.
Santos, N.R., J.V.E. Katz, P.B. Moyle, and J. H. Viers. 2013.A programmable information system for management and analysis of aquatic species range data in California. Environmental Modeling & Software 53:13-26. http://dx.doi.org/10.1016/j.envsoft.2013.10.024
Zimmerman, J.K., Carlisle, D.M., May, J.T., Klausmeyer, K.R., Grantham, T.E., Brown, L.R. and Howard, J.K., 2018. Patterns and magnitude of flow alteration in California, USA. Freshwater Biology, 63(8):859-873.
In 1972, the U.S. Clean Water Act (CWA) created a permit system for point source discharges to navigable waters of the United States – rivers, lakes, and coastal waters – with the goal of restoring and protecting their water quality. Typically, these permits are issued by the U.S. EPA or through state agencies to dischargers of wastewater, e.g., from urban and industrial wastewater treatment plants and to other dischargers of potentially contaminated water that reach streams by a pipe or similar conveyance. The goal was to provide some degree of regulatory oversight over such discharges. In California, the State Water Resources Control Board implements the federal Clean Water Act using its authority under the Porter-Cologne Water Quality Control Act (Water Code, §13000 et seq.). Under the CWA, neither EPA nor the states are required to issue permits for pollutant discharges into groundwater or to nonpoint source dischargers.
This week, the Supreme Court decided on a case involving discharge from a wastewater reclamation facility owned and operated by the County of Maui. In this case, the facility discharged 3 to 5 million gallons of treated wastewater per day into four injection wells about half a mile from the ocean. Recent research showed that much of the injected waste eventually discharges to the ocean. Environmental groups sued the county for not obtaining a CWA permit, arguing that point source discharge of pollutants that eventually reach surface water is governed under CWA. All sides agreed that the case at hand involved a point source of pollutant discharge and that the pollution eventually reached the ocean. The disagreement was whether the CWA requires the permit only if the pollutant discharge is directly into surface water, as argued by the defendants (a “bright-line test”). Environmental groups argued that even if the pollutant discharge is via groundwater to surface water, the CWA permit must be obtained. The district court and the Ninth Circuit court ruled in favor of the plaintiffs. The Ninth Circuit court held that permits are required when “pollutants are fairly traceable” from the point source to surface water.
In its final 6-3 decision, the Supreme Court majority now rejects both sides’ arguments as too extreme and returned the case to the lower courts with further guidance. On the “bright-line test”, Justice Breyer, writing for the majority, wrote “we do not see how Congress could have intended to create such a large and obvious loop hole in one of the key regulatory innovations of the Clean Water Act.” On the “fairly traceable” approach, the opinion stated that such interpretation “would require a permit in surprising, even bizarre circumstances”.
Instead, the Court decision introduces the concept of a “functional equivalent of a direct discharge” as a guideline for when a point source discharge must obtain a permit. It cites the case of an injection well receiving pollutant discharge that then travels a few feet through groundwater into navigable waters as a clear case of “functional equivalent” to direct discharge. But it rejects the notion that such a “functional equivalent” exists in a case with “100 year migration of pollutants through 250 miles of groundwater to a river” and “likely does not apply” if “the pipe ends 50 miles from navigable waters”. The Court acknowledges that the concept of “functional equivalence” as the Court’s guideline leaves many point source discharges to groundwater somewhere between these extreme cases. It relegates consideration of those cases back to regulators and lower courts, suggesting they consider the various groundwater flow and transport factors underlying individual cases – travel time and distance in particular, but also soils and geology, geochemical reactions, the locations where pollutants subsequently enter navigable waters, and “the degree to which the pollution (at that point) has maintained its specific identity.”
Importantly, the majority opinion does not expect a “vastly” expanded scope of the CWA, such that permits would be required, e.g., for the country’s 20 million septic systems. It does so in two ways: by emphasizing (and affirming) the long history of CWA implementation, which has, at times, required permits even if pollutant discharge was via groundwater into surface waters, but not under other circumstances. And, secondly, both the majority and dissenting opinions repeatedly underscore the important role and sovereignty of states in regulating discharges to groundwater and nonpoint source pollution (groundwater pollutant discharge to surface water is sometimes considered nonpoint source pollution of surface water).
The decision will not make it easier than in the past for either regulators or lower courts to make their determinations as to whether a point source pollutant discharge to groundwater that eventually affects surface water is subject to a CWA permit. But the decision sides squarely with the use of science. And it shows a remarkable acknowledgement of hydrologic sciences and the interconnectedness of surface water and groundwater: “Virtually all water, polluted or not, eventually make its way to navigable water. This is as true for groundwater.” Perhaps this statement missed the nuance that some groundwater, particularly in the western U.S., will instead be pumped by wells onto crops or pulled by plant roots from the water table to be evapotranspired into the atmosphere. But it underscores that the court made its decision knowing and applying hydrologic science. “Given the power of modern science, The Ninth Circuit’s limitation, ‘fairly traceable’, may well allow EPA to assert permitting authority over the release of pollutants that reach navigable waters many years after their release […] and in highly diluted forms.”, an application that the justices find inconsistent with the CWA.
The dissenting opinion of Justice Alito rejects the introduction of the “functional equivalence” concept as too vague and inconsistent with the language of CWA. Given the authorities of states on matters of groundwater and nonpoint source pollution, he supports the “bright-line test”. But importantly, Justice Alito instead refers to the definition of “point source” as a means to avoid the loopholes cited in the majority opinion as reason to reject the “bright-line test”: He points out that, according to CWA, “point source[s] include [….] ‘any discernible, confined and discrete conveyance… from which pollutants … may be discharged.’ §1362(14).” The opinion continues to describe how the pathway created by pollutant discharge from a pipe onto a beach and ending in the ocean” or many of the cases that trouble the Court” would easily be covered by applying common definitions of “conveyance”, “discernable”, and “confined”. Groundwater hydrologists may further point out something not mentioned and perhaps not considered by Justice Alito: that we do have scientific tools (as referred to by the majority opinion) to similarly describe some groundwater pathways as a conveyance that is indeed discernable and confined, “i.e., held within bounds”. So perhaps Justice Alito’s argument, from a scientific perspective, would in practice not be substantively different from the scientific criteria that the majority opinion associated with defining “functional equivalent” point source discharge. Such an interpretation would add further support and a consistent angle to the overall spirit of the Court’s decision.
The Maui decision is already having a ripple effect in other areas of environmental
concern. Environmentalists have long been advocating against the use of coal ash impoundments—open pits for disposal of toxic byproducts left over from burning coal. Many of these byproducts have allegedly moved from these impoundments through groundwater into streams and rivers. Prior to the decision in Maui, power companies argued the CWA permitting program was inapplicable to impoundments. But the Maui decision will likely lend weight to these challenges.
The Maui decision also will likely impact litigation over the federal administration’s repeal of the Water of the United States rule, a regulation under the Obama administration which clarified the views of the Environmental Protection Agency and the U.S. Army Corps of Engineers about the reach of the Clean Water Act. In this repeal, this administration specifically stated, in response to commenters, that “A groundwater or subsurface connection could also be confusing and difficult to implement, including in the determination of whether a subsurface connection exists and to what extent.” U.S. Army Corps of Engineers and Environmental Protection Agency, The Navigable Waters Protection Rule: Definition of ‘‘Waters of the United States,” 85 Fed. Reg. 22,250, 22,313 (Apr. 21, 2020). Promulgated by the agencies before the Maui decision came out, the agencies will likely have to wrestle with the Maui decision in subsequent challenges.
While the decision leaves some previous uncertainty over the interpretation of the CWA, and perhaps adds some, California dischargers are unlikely to face additional regulation under this decision. Under the Porter-Cologne Water Quality Control Act, California already requires permits for discharges to groundwater, even if they don’t meet the “functional equivalent” test outlined by Justice Breyer’s majority opinion. California regulators may need to adjust their approach to reflect that some of these permits will also serve as CWA permits under the state’s authority, but this should not impose significant new burdens on regulated entities. California’s robust implementation of a strong groundwater quality regulatory program, implementing state laws (including the Sustainable Groundwater Management Act, SGMA) and other federal laws governing discharge of pollutants to groundwater (Safe Drinking Water Act, Toxic Substances Control Act, Resources Conservation and Recovery Act, state and federal Superfund programs) puts it in an excellent position to have little to worry about a new layer of bureaucracy and restrictions.
The decision’s reliance on strong groundwater science marks another significant step in the emerging integration of groundwater and surface water. The California courts and legislature have long regarded surface water and groundwater as legally distinct, but over the last decade that legal fiction has begun to break down. In 2014, SGMA explicitly recognized the relationship between groundwater and surface water, requiring groundwater managers to avoid significant and unreasonable adverse impacts on beneficial uses of surface water. In 2018, a California appellate court ruled that the public doctrine applies to groundwater extraction if it adversely impacts a navigable waterway. This decision validates the hard work of water scientists working to protect critical freshwater systems in the context of integrated watershed and water resources management, including efforts to protect many of these freshwater resources that depend on high quality groundwater discharge. And it reminds us to keep hard at working to achieve the larger vision of the Clean Water Act.
Professors Harter and Tai were both authors of an amicus brief in this Supreme Court case.
Thomas Harter is a Professor of Hydrologic Sciences and a Cooperative Extension Groundwater Specialist at the University of California, Davis. He is currently Acting Director of the UC Davis Center for Watershed Sciences and Chair of the Hydrologic Sciences Graduate Group.
Steph Tai is a Professor of Law at the University of Wisconsin Law School. Their research focuses on areas of science, risk, and environmental and food regulation.
Karrigan Bork is an Acting Professor of Law and an Associate Director of the Center for Watershed Sciences at the University of California, Davis. His research focuses on water law, environmental law, and natural resource conservation.
By Andrew L. Rypel, Gabriel Singer, and Nann A. Fangue
“You can’t design a worse evolutionary strategy for the Anthropocene”
There are many variants on this quote, and we’ve heard them often in reference to the status of native fishes in California and other freshwater organisms worldwide. Indeed, the statement rings true for Pacific salmon, but especially spring-run Chinook salmon (Oncorhynchus tshawytscha) in California. And although the current situation certainly looks bleak overall for endangered salmon (Moyle et al. 2017), there are signs in a few corners that the arrow may finally be pointing up. For the last four years, our team at UC Davis has been conducting scientific studies on reintroduced spring-run Chinook salmon in the San Joaquin River and we wanted to take a minute to share some of what we’ve learned. Plus, everyone loves a good comeback story right?
Primer on the life-history of spring-run Chinook salmon
The complicated life-histories of Chinook salmon in the Pacific are well-known. Indeed they are a frequent topic of blog posts here! (examples, 1, 2, 3). Living as adults in the Pacific Ocean and migrating into freshwater tributaries, adults spawn and subsequently die leaving their carcasses to fertilize freshwater ecosystems with marine-derived nutrients. Young salmon must outmigrate from freshwater habitats to the ocean (and survive!) where they feed and live as adults. In California, we think of late summer and into fall, and maybe even into winter as prime time adult Chinook salmon migration time. But, spring-run Chinook salmon are different. These fish enter freshwater in spring months as sexually immature adults, and historically migrated long distances upriver to coldwater refuges in the mountains. Here, they “oversummer”, often congregating in deep coldwater plunge pools high in the landscape where they survived on their fat reserves, which dwindled as they continued to mature. When rains and flows increase in the late fall, barriers to movement suddenly become passable and fish would migrate further into the high California landscape to spawn in the fall. When you consider this life-history, and the current human-dominated landscape of California (think dams built without fish passage, climate change, landscape alterations), it is little wonder that this species (technically an “ESU, Ecologically Significant Unit”) has declined to where it is listed under the CA and US Endangered Species Act. Yet, spring-run Chinook salmon are full of surprises. Here’s some of them:
Surprise 1 – Spring-run Chinook salmon historically were co-dominant with the fall-run in the Central Valley and in some years may even have exceeded the fall-run in overall abundance. Today, we tend to consider fall-run Chinook salmon as the main run of salmon in California, but alas, it was the spring-run that originally predominated in the early commercial salmon fishery due to its great abundance, wide distribution and higher food quality. In one year alone (1883), at least 567,000 spring-run salmon were reported caught in the commercial fishery, not to mention all the fish that escaped the fishery and spawned in their home streams. Through the 1880s, total commercial harvests (composed primarily of spring-run fish) generally hovered around 5 million to 10 million pounds — which, at an average weight of 16 pounds per salmon, would have equated to about 310,000 to 625,000 salmon. Current valley-wide numbers oscillate between only a few thousand to upwards of 25,000 adults (Fig. 2).
Surprise 2 – While it is hard to imagine now, the San Joaquin River at one time contained the most abundant population of spring-run Chinook salmon in the Central Valley, perhaps due to the extirpation of all the other great spring-run populations originally found throughout the Valley (Yoshiyama et al 1998). Most of these fish spawned in the upper reaches of the watershed in the Sierra Nevada where strong coldwater habitats allowed fish to over-summer as described above. Following the completion of Friant Dam, spring-run Chinook salmon in the San Joaquin River were predictably extirpated in rapid succession. Identical stories of dams built without fish passage and subsequent salmon declines exist for every major river draining into the Central Valley. Yet in addition to blocking access to coldwater habitat in the Sierra Nevada, completion of Friant Dam and a chain of dams upstream (e.g., Kerckhoff Dam/Millerton Reservoir) also facilitated diversion of high proportions of water from the San Joaquin River such that ~ 60 miles were left completely dry when the project was completed (Matthews 2007).
Surprise 3 – Despite continued degradation of the river (Fig. 3), and its status as perennial contender for “America’s most endangered river”, spring-run Chinook salmon have been on the comeback trail for the last five years. Much of this success is largely due to a massive habitat restoration and reintroduction effort, spear-headed by the San Joaquin River Restoration Program (SJRRP). The SJRRP has developed a comprehensive reintroduction strategy for spring-run Chinook salmon intended to overcome the various obstacles that impede reestablishment of a viable spring-run Chinook salmon population. Habitat projects include restoring connectivity in the river, increasing flows to provide suitable habitat to complete all phases of the life cycle, and removal and reconfiguration of structures that obstruct movement of salmon. The phased goals of the program include reintroduction of spring-run Chinook salmon (supported by a conservation hatchery operated by CDFW), establishment of self-sustaining local populations under contemporary river conditions, and finally long-term maintenance of a population of 30,000 spawning adults with negligible hatchery influence.
It is of note that spring-run fish from the Feather River Hatchery were used to initially jumpstart the conservation hatchery broodstock for the San Joaquin River. Thus, we can never truly “bring back” the original upper San Joaquin spring-run – a notable consequence of extinction overall. However, a recently published genomic study on Central Valley Chinook salmon (Meek et al. 2020) revealed that Feather River Hatchery spring-run have distinctive genetic elements that set it apart from the two other Central Valley spring-runs (i.e., Mill/Deer Creek, and Butte Creek) as well as from the Feather River Hatchery fall-run. This finding in turn suggests the Feather River Hatchery spring-run likely retains ancestral genetic elements from the original Feather River spring-run varieties. Hence, the new reintroduced San Joaquin spring-run population is aiding in preservation of Feather River spring-run ancestry, but also, overall genetic diversity of Central Valley Chinook populations – this is a good thing.
Science to inform adaptive management of spring-run Chinook salmon
Over the last 4 years, our team has been developing science that can be used to facilitate adaptive management of reintroduced spring-run Chinook salmon in the San Joaquin River. The centerpiece to this work has been a set of focused acoustic telemetry studies on juvenile salmon released each spring. Beginning each year in early March, our team usually tags 750 juvenile spring-run Chinook salmon produced at the Salmon Conservation and Research Facility (SCARF; Friant, CA) with miniature Juvenile Salmon Acoustic Telemetry System (JSATS) transmitters. Similar to a recent blog, these transmitters produce sounds that are then “heard” by receivers maintained by our team throughout the river (Fig. 4). Fish with uniquely coded transmitters swim past receivers and data are registered allowing us to study survival rates, routing and other fish behaviors of interest. The JSATS transmitters are the smallest available on the commercial market, allowing us to track fish as small as ~72mm in length, although we prefer to tag larger smolts.
Currently, spring-run Chinook salmon are confined to only the lower San Joaquin River (below Friant Dam). Therefore, we track fish through this area which includes the lower region of the Restoration Area, but also continues through the Sacramento-San Joaquin Delta, San Francisco Estuary, and entrance to the Pacific Ocean. We also maintain (fancier and more expensive) real-time receivers at the federal and state pumping facilities which provide a rapid window into how many juvenile fish are being entrained and salvaged at the water pumping facilities. These receivers transmit data in real time via cell phone towers. See example of real-time telemetry data from this year’s spring-run tagging.
With three years of data now in the bag, some patterns are notably clear. First, as is typical with juvenile salmon in the Central Valley – water matters! Years during which there was increased precipitation and high flows, survivorship to the ocean was higher. In 2017 (a wet year – remember Oroville Dam!), we estimated out-migration survival to the Golden gate at 2-5%, but in 2018 (a drier year) survivorship plunged to only 0.5%. In a wetter year, 2019 survivorship increased again to 5%. In 2020, real time receivers at Benicia Bridge estimate that so far only 0.5% of our fish have successfully out-migrated to the ocean – ouch again! As a comparison, telemetry studies for other runs of Chinook salmon in the Sacramento during 2019 suggested outmigration survival rates upwards of 15-20%. Our data therefore indicate survivorship is uniformly low for salmon in the San Joaquin River overall, and that flows here probably really matter for the fish. Most of the tagged fish that enter the interior Delta simply don’t make it out.
Finally, we have found that many of our tagged fish are plucked out of the river at the fish salvage facilities located at the Central Valley Project and State Water Project (pumping facilities). Interestingly, these fish often have higher survivorship to the ocean versus fish remaining in the mainstem San Joaquin River or freely swimming through the interior Delta. This pattern is likely not because being salvaged is “good for fish” but rather, because upon salvage, fish are physically trucked around the interior Delta to the San Francisco Bay. Previous studies on fall-run salmon smolts in the system found highly similar patterns (Buchanan et al. 2018). Furthermore, a temporary fish barrier is often installed by the Department of Water Resources (DWR) at the head of Old River to prevent fish from being drawn towards the pumping facilities (DWR 1992). Yet it now seems possible that this barrier, originally installed to prevent fish from accessing an assumed low survival route in low discharge years, may sometimes actually block access to the highest survival out-migration pathway (salvage). It is notably sad and ironic perhaps, that the quality of habitat in the lower river is so poor that the best migration path for salmon appears to be as a salvaged fish, trucked around the Delta by DWR or BOR staff.
As we continue to gain data on the biology of reintroduced salmon in the San Joaquin River, we will be able to provide increased information valuable for conservation. For example, we are conducting focused experiments on specific areas of the interior delta that we think may be especially problematic for salmon smolts (e.g., Frank’s Tract). We are also conducting innovative studies on the physiology of salmon smolts experimentally exposed to different parts of the river. Finally, we are conducting in-depth habitat assessments to further inform why there are major “hotspots of death” for salmon in the lower portions of the ecosystem. In the future, adding more upriver habitat to the current migration corridor for spring-run may be worth consideration. For example, historically, the very best spring-run Chinook habitat was in the area where Kerckhoff Dam (Millerton Reservoir) now stands, upriver from Friant. While these areas are now mostly flooded, remnants of deep pool habitat do exist below Kerckhoff Dam, making restoration a possibility in these areas. If these pools can be managed for coldwater through summer months, small runs of spring-run Chinook salmon above Friant may also be possible.
Finally, what we have encountered all along the way has been a constant dedication to the fish and ecosystem from biologists of all stripes at agencies, universities, fishing groups and others. We work hand-in-hand with a number of agencies conducting concurrent telemetry studies in the Sacramento River and Delta, and are constantly impressed by the professionalism and dedication needed to help recover our fish populations. It is heartening that against all odds, spring-run Chinook salmon are staging a comeback (albeit small currently) in one of the most endangered rivers in the USA. We are proud to be part of these interdisciplinary studies that provide, not only information needed immediately for conservation, but also as a training ground for the future of fisheries biology. There are so many to praise for these advances.
Azat, J. 2019. GrandTab 2019.05.07 California Central Valley Chinook Population Database Report. California Department of Fish and Wildlife, Sacramento, CA USA.
Buchanan, R.A., Brandes, P.L., Skalski, J.R., 2018. Survival of Juvenile Fall-Run Chinook Salmon through the San Joaquin River Delta, California, 2010–2015. North American Journal of Fisheries Management 38: 663–679.
California Department of Water Resources. 1992. South Delta Temporary Barriers Project: monitoring, evaluation, and management program. California Department of Water Resources, Sacramento, CA USA.
Matthews, N. 2007. Rewatering the San Joaquin River: A Summary of the Friant Dam Litigation. Ecology Law Quarterly 34(3): 1109–1135.
Meek, M.H., M.R. Stephens, A. Goodbla, M. May, and M.R. Baerwald. 2020. Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence. Canadian Journal of Fisheries and Aquatic Sciences 77: 534-547.
Moyle, P. B., R. Lusardi, and P. Samuel. 2017. State of the Salmonids II: Fish in hot water. Status, threats and solutions for California salmon, steelhead and trout. University of California-Davis, CA USA.Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.
Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.
This research is being funded by the Delta Science Council, with additional support from the California Department of Fish and Wildlife (CDFW) and the US Fish and Wildlife Service (USFWS). Our larger team of scientists at UC Davis working on this project includes Dennis Cocherell, Colby Hause, Leah Mellinger, Sarah Baird, Michael Thomas, Amanda Agosta, Heather Bell, Matthew Pagel, Emily Jacinto, Mackenzie Miner, Wilson Xiong. We also thank past scientists at UC Davis including A. Peter Klimley and Eric Chapman for their important contributions in the early years of this work. Lori Smith and Pat Brandes (USFWS), Don Portz (SJRRP), Towns Burgess (SJRRP), John Kelly (CDFW), Matt Bigelow (CDFW), and Josh Isreal (USBOR) have all been critical to supporting and continuing this work. We thank Peter Moyle, Ronald Yoshiyama and Towns Burgess for reviewing earlier versions of this blog.
Striped bass are an iconic and recreationally important fish species throughout the United States, including within their native range on the Atlantic Coast. Based on their value as a sport fish and as table fare, striped bass were one of the early introductions to the San Francisco Estuary (SFE). Their life-history and abundance within the SFE has been studied as much or more than any other fish present in the system, with only Chinook salmon, and more recently Delta smelt, approaching the same level of interest. Given the historical resources dedicated to monitoring and studying striped bass in the SFE, the question must be asked; why don’t we know more about what they’re doing in the Pacific Ocean?
The magnitude of striped bass migrations along the North American Atlantic Coast is well-known. Believed to be cued by increased ocean temperatures during summer months, a large proportion of Atlantic Coast striped bass migrate north every summer in search of productive feeding grounds. This behavior not only provides valuable food resources to migrants, it also exposes individuals to mortality risk from recreational and commercial fisheries. In California, striped bass’ introduction to the SFE occurred in 1879, and the first recorded catch was just one year later in Monterey Bay (Smith 1895). In relatively rapid order, the species became fully established and supported a large commercial fishery (Scofield 1931). Likewise, multiple permanent and transient populations have established via coastal migrations in estuaries up and down the Pacific Coast. One such population, in Coos Bay, Oregon, became large enough to support a commercial fishery for several decades before it collapsed, apparently due to inbreeding (Waldman et al. 1998).
Limited research has gone into understanding what conditions are responsible for striped bass venturing into the Pacific Ocean. Past studies have relied mainly on catch data from commercial party fishing boats that fish within the SFE and just outside of the Golden Gate. These data show that catch of striped bass in the Pacific Ocean increases during periods of unusually warm sea surface temperatures (Radovich 1963, Bennett and Howard 1997). Unusually warm, however, has shifted in meaning as climate change progresses. For example, extreme El Niño events that bring warm water to the Pacific Coast are forecasted to increase in frequency as the global climate warms (Wang et al. 2017).
Increased catch of striped bass in the Pacific Ocean during El Niño events, the establishment of Oregon populations, and the annual Atlantic Coast migrations indicate that Pacific Coast migrations have and will continue to occur. However, the specific dynamics and repercussions of this behavior for the SFE population are largely unknown. Along the Atlantic Coast, it is well-established that large female striped bass migrate. These same individuals also produce the highest number and quality of eggs. Thus, if female mortality is high in the Pacific Ocean, or if individuals permanently emigrate to other estuaries, a loss of juvenile production may occur. Bennett and Howard (1997) speculated that these dynamics may at least partially explain the long-term decline of striped bass populations within the SFE.
While the results from party boat data are compelling, these data are hard to interpret given changing effort and fishing gear over time. In addition, these results do not provide much information outside of the heavily fished areas near the Golden Gate and only a single data point for any given individual. My colleagues and I started the UC Davis Ocean Striped Bass Project with the goal of better understanding what large female striped bass are doing within the SFE and along the Pacific Coast. Part of this project involves tracking movements of individuals using a combination of acoustic telemetry and otolith microchemistry.
Acoustic telemetry is a technical term for what is essentially tracking animals using tags that emit coded high-pitched sounds. The tags used in this study emit a signal at a frequency far higher than what a human can hear, and which can effectively transmit a unique identification code through both freshwater and saltwater. When a tagged fish swims by an acoustic receiver (hydrophone), of which there are many deployed throughout the SFE and the rivers that flow into it, its tag code is recorded along with the time and date. Using this technology, we can track tagged fish for up to seven years throughout the SFE and upstream rivers.
But what about coastal migrations? As a part of the Ocean Striped Bass Project, a total of 22 acoustic receivers have been deployed from zero to three nautical miles offshore at Point Reyes and Point San Pedro, just north and south of the Golden Gate, respectively (Fig. 3). These receivers act as “gates” to migratory individuals, listening for tagged fish as they pass on their way north or south. If an individual is recorded only once at either of these gates, we know it either died or emigrated to another estuary and can be counted as “lost” to the SFE population.
Why do we care what happens to striped bass in the Pacific Ocean? Striped bass are an extremely important recreational species within the SFE and upstream rivers; they are a cultural, consumptive, and economic resource for thousands of people. They are also an important indicator species because they require many of the same environmental conditions as vulnerable native species, such as longfin smelt and delta smelt, that now exist at population levels too low to effectively track. By not knowing the coastal migration dynamics of large female striped bass, we limit our ability to identify drivers of population declines more broadly. Finally, while the effects of predation by striped bass in the SFE and upstream rivers is hotly debated, they may be a more tangible threat to native species in the small estuaries up the California and Oregon coasts. Striped bass are truly novel to these estuaries, and if climate change increases their colonization potential, native species declines may occur.
If you would like to know more about the Ocean Striped Bass Project please contact me, Dylan Stompe, at firstname.lastname@example.org. This project is funded by the California Department of Water Resources.
Dylan Stompe is a Ph.D. student based at the Center for Watershed Sciences.
Bennett, B., and L. Howard. 1997. El Niños and The Decline of Striped Bass. IEP Newsletter 10(4):17–21.
Radovich. 1963. Effect of ocean temperature on the seaward movements of striped bass, Roccus saxatilis, on the Pacific coast. California Fish and Game 49(3).
Scofield, E. C. 1931. The Striped Bass of California (Roccus lineatus). California Fish and Game Fish Bulletin 29.
Smith, H. M. 1895. A Review of the History and Results of the Attempts to Acclimatize Fish and Other Water Animals in the Pacific States. U.S. Fish Commission Bulletin 15.
Waldman, J. R., R. E. Bender, and I. I. Wirgin. 1998. Multiple population bottlenecks and DNA diversity in populations of wild striped bass, Morone saxatilis. Fishery Bulletin 96:614–620.
Wang, G., W. Cai, B. Gan, L. Wu, A. Santoso, X. Lin, Z. Chen, and M. J. McPhaden. 2017. Continued increase of extreme El Niño frequency long after 1.5 °C warming stabilization. Nature Climate Change 7:568–572.
by Peter Moyle, Center for Watershed Sciences, UC Davis
Delta smelt are an endangered species and the latest estimates of their numbers indicate they will likely not be around much longer as wild fish. When I first started working on them, in the 1970s, they were abundant and frequently caught in various sampling programs. One of my regrets is that I never ate any that we caught, despite the fact that smelt in general are highly regarded as food fish. Indeed, a memorable experience from my high school days in Minnesota was driving up to the North Shore of Lake Superior with friends and spending a night dip-netting rainbow smelt in the freezing water. We built a fire on the beach and luxuriously fried the smelt in butter. We ate them heads and all, a tradition I learned from my father. Delicious.
Historically, the principal smelts of the San Francisco estuary were longfin smelt, delta smelt, and, probably, surf smelt; the latter is mostly a marine species. Archaeological evidence suggests smelt were caught and eaten on occasion by the indigenous peoples of the region. In the latter half of the 19th century, there was a smelt fishery in the estuary, but it was poorly documented, presumably because the fish were mainly caught and consumed by Chinese immigrants. In Jordan and Evermann (1896), however, the authors characterized the “pond smelts” – a group of related species that includes delta smelt, as “…sweet little fish, delicious as food” and again in 1923 as“delicious and excellent little food fish…”
I encountered delta smelt (and longfin smelt) on a regular basis after the UC Davis project began to monitor fish populations in Suisun Marsh in 1979. They were commonly captured in the otter trawls that we used monthly at multiple sampling stations. Given that we only trawled for 5 or 10 minutes at each locality, with a trawl-net dragged along the bottom (smelt are pelagic), it is a tribute to smelt abundance that enough were caught to make a meal. At that time, they were not a species of concern for any agency, much less classified as endangered.
I was reminded of their lost abundance then when Sonia Cook recently sent me some photos she had taken of sampling the marsh on November 16, 1982. Sonia at that time was a technician in the Botany Department who was interested in fish and enjoyed going out with my sampling crew as a volunteer. Being an adventurous person, she asked if she could bring some smelt home for dinner that night. The 35-40 smelt that Sonia kept were just part of the day’s catch. They are shown in the photo she took of the smelt that she kept.
This got me thinking about how badly we have managed the smelt’s pelagic habitat since that time. Now the greatest fear of many fish sampling programs is that one or two delta smelt will be caught, which could shut down an entire program (like the one in Suisun Marsh) because of take restrictions stemming from the Endangered Species Act. Think of how much better off the Delta ecosystem would be if the protections for smelt existed to protect a fishery, not the few last individuals. I am sad that I missed the opportunity to dine on delta and longfin smelt. But that is the goal we should be working towards: restoring delta and longfin smelt to a point where they can be harvested in the San Francisco Estuary and watershed…or at least contribute significantly to the food webs as they once did.
Jordan, D.S. and B. W. Evermann. 1896. The Fishes of North and Middle America. Bulletin of the United States National Museum 47, Part 1.
Jordan, D.S. and B. W. Evermann. 1923. American Food and Game Fishes. New York: Doubleday, Page & Co.
Today the Megalopolitan Water District of California (a consortium of southern California and Bay Area urban water suppliers) proposed building a new aqueduct to take water from the Sacramento River to Bay Area and southern California cities. The aqueduct, depicted below, would avoid the subsurface uncertainties of a Delta tunnel, ease monitoring and inspections, and avoid interference with fish and wildlife migrations in and through the Delta.
The proposal states, “For centuries, major Mediterranean urban areas relied on aqueducts to supply waters to sustain their economic and cultural prosperity. For decades, we have built canals and pipelines in California for this purpose. Our cities in southern California and the Bay Area have concluded that a more classical Delta conveyance solution should be sought if the state’s currently proposed tunnel is rejected.”
Proponents stated that an above-ground aqueduct would allow all sides of the Delta debates to “win”. There would be no tunnels or peripheral canal, there would be water for cities that does not reverse flows for fish in the Delta, and there would be highly-visible attractive naming opportunities. Indeed, if constructed in the old style, each southern California and Bay Area resident using the water could have their name engraved on one of the aqueduct’s many stones, with each Delta land owner immortalized with the naming of an arch.
Donald Hightower, a spokesman for the Bay Area Water Suppliers Alliance (BAWSA), noted, “Major State Water Project facilities were built with great pride and extensive staffed public visitor centers. Sadly, these visitor centers are now largely closed, and visitors can hardly see some of California’s most important public infrastructure. An above ground aqueduct across the Delta would provide a visible monument to California’s successes in water management, from miles away, and a tourist attraction for the Delta economy.”
The Transportation and Recreation Authority of California (TRAC) is considering joining the proposal, seeing it as a potential water slide to enjoyably increase public transport capacity from Sacramento to the Bay Area.
“Today, we proposed an above-ground aqueduct across the Delta that will define the Delta as a very special place, the home of the world’s longest above-ground aqueduct. All aspects of this project will be above ground and visible, from construction to operations,” said Geoffrey Kiteflyer, the retiring Director of the District. “I hope this project serves as long as Valens’ did for Constantinople and Istanbul.”
Some expressed skepticism, noting the high expense of the project and the low flows supplied by such aqueducts in ancient times, compared to modern expectations. “Valen’s aqueduct served one of the world’s largest cities in 400 AD with less than 100 cfs of flow. That was a lot then, but is not so much now, compared with the Delta pumps 15,000 cfs current capacity,” said former DWR employee Sam Gei. Several environmental groups, although not unhappy about the reduced Delta diversions, expressed concern for the effects of an above-ground aqueduct on waterfowl flight paths and solar shading of native plants, and are organizing themselves into a group called “Delta Arch-Enemies”.
Past solutions for Delta conveyance have concentrated on taking water through the Delta, around the Delta, or under the Delta. Perhaps it is time to look at taking water over the Delta.
With or without an aqueduct, the Delta is a beautiful region with some problems which cannot be solved perfectly.
There was not a “Miracle March” to follow California’s precipitation “Flat-line February.” Instead, we’ve had a “Meh March.”
With the near-end of its wet season, California’s 2020 water year is and will be dry. The Northern Sierra 8-gage Precipitation Index is now about 25 inches, and might increase about 10% more by the end of the water year. This would place the 2020 water year somewhere between the 3% – 7% driest year on record for this index (98 years). Other precipitation and snow statistics for California tell a similar story.
Sacramento Valley runoff for 2020 also will be greatly reduced (see first figure). Other basins in California are similarly dry.
Just how dry is 2020?
On the whole, with about 50% of average precipitation and snowpack, California can expect dry conditions for its forests and upland habitats, particularly later in the summer as soil moisture is depleted. These impacts will be somewhat dampened because recent years have not been terribly dry, so there is more soil moisture and groundwater. Next year could be different.
From Figure 1 above, we can expect about 50% of average stream runoff, maybe a little less. This of course has implications for reservoir inflows, hydropower generation, agricultural and urban water supplies, and aquatic and wetland habitats. Fortunately, most California reservoirs are still pretty full and many groundwater supplies have at least partially recovered from the 2012-2016 drought. So for many water users, the first dry year is not so bad. Still, there will be impacts.
Is the 2020 water year a drought?
Maybe for some, but mostly not yet.
In some pragmatic senses, a drought is a dry event that water users are not prepared for.
For some users and uses, a single dry year is a drought. This includes upland habitats which depend on soil moisture to get through our long dry season, more junior summer and fall water users on streams without reservoirs, rural water users with marginal supplies subject to groundwater depletion, and wetland and aquatic habitats, especially if they lack supplemental water supplies.
Most of California’s human water users have become prepared for dry years and droughts over the last 150 years by adopting a portfolio of infrastructure and actions, including irrigation systems, water storage, groundwater, water trading, and water conservation practices that sustain their activities through California’s annual 6-9 month drought (worse annually than most of the US ever sees). For most major cities and many agricultural areas, these preparations also suffice for most multi-year droughts (Lund et al. 2018).
The difficulties of managing drought increase with a drought’s duration. Most of California, even ecosystems, are adapted to a long single dry season, preceded by a wet season. A dry year extends and reduces water stored for this dry season. Sequential dry years further reduce the water stored in soils, reservoirs, and groundwater for dry-season water demands.
By the third and fourth dry years, ecosystems and human water supply systems go from straining to breaking. In long multi-year droughts, cities can be forced to ration water, farmers must consider sacrificing their most profitable crops, more rural drinking water supplies are left dry by declining groundwater, and salmon runs can no longer rely on stored cold water.
Is 2020 the beginning of a major statewide drought?
Maybe. The plot below shows each year in a 113-year unimpaired Sacramento Valley streamflow record plotted against the previous year’s unimpaired streamflow. There is only a slight tendency for a dry year to be followed by another dry year (a previous post shows this another way). The dryness of the previous year explains less than 1% of how wet the next year will be. So the probability of this dry year being the beginning of several years of drier-than-average conditions is slightly more than 50%.
What should be done?
Prepare for this year to be dry (a certainty) and prepare for next year to be dry (fairly likely).
Preparation is key to reducing the impacts of dry years (Lund et al 2018). Many with dry-year contingency plans will begin their implementation. For those without prepared plans, now is a good time to start making plans and preparations. Active preparations should include:
Reducing less crucial water uses, particularly where water can be directly or indirectly stored.
Support and prepare to support wetland and aquatic ecosystems, including and especially the Delta.
Inventory regional groundwater availability, and think about SGMA consequences of drought.
Work with your neighbors to prepare.
The various COVID-19 shut-downs and slow-downs are likely to make late preparations more difficult, especially where plans, such as those for the Delta, ecosystems, and groundwater, require coordination among many agencies and entities, now with few and smaller face-to-face meetings and competing with a pandemic for attention and resources.
Pandemic concerns will require managing water and ecosystems amid a drought of attention and resources and viral distractions.
Also prepare for next year to be wet and have flooding, because this can easily happen too.