by Bronwen Stanford, Julie Zimmerman, Kris Taniguchi-Quan, Ted Grantham, Sarah Yarnell, Alyssa Obester, Eric Stein, Jessi Ayers, Alex Milward

As recent droughts have highlighted, groundwater overuse is a serious problem in California. Overdraft is drying shallower domestic and municipal wells, dewatering groundwater dependent ecosystems (Rohde et al. 2021), and necessitating expensive infrastructure repairs. As climate change reduces snowpack and increases risk of drought, reliance on groundwater will grow (Mount et al. 2018).

To meet these challenges, the Sustainable Groundwater Management Act (SGMA) has helped focus attention on strategies to manage our groundwater use more sustainably, including efforts to replenish groundwater stores. Flood managed aquifer recharge, or Flood-MAR, is a strategy to intentionally create flooding over dormant or fallow crop fields, rangelands, recharge basins, or floodplains during high flows so that water infiltrates to recharge aquifers. By storing water underground in wet years, we can improve water availability in dry years, supporting water users and refilling aquifers. There also can be a host of ecological benefits, particularly for Flood-MAR projects that reintroduce water to historical floodplains and reactivate wetland and riparian habitats.

However, the way that we implement recharge matters. First, recharge needs to help balance our water budget, particularly in overdrafted groundwater basins. Like the paradox of irrigation efficiency (Grafton et al. 2018), there is a risk that increasing recharge will be used to delay a movement towards groundwater sustainability. Recharge viewed as a “new” source of supply can be used to justify current – or expanded – water use, forgoing benefits of storing water to recover depleted aquifers and prepare for dry periods. If recharge is not coupled with actions to manage and reduce demand, then adverse impacts of falling groundwater levels on communities, ecosystems, and infrastructure are likely to persist. We would miss an opportunity to build climate resilience and instead continue to worsen the vulnerability of our water supply system.

Second, we need to avoid causing harm to already highly stressed rivers and streams. Combining existing summertime surface water use with additional large-scale wet season diversions could have dire impacts for aquatic ecosystems. Research has increasingly shown that wet years and wet seasons are critical to survival of native salmonids (e.g., Michel 2019, Notch et al. 2020), and almost all rivers and streams lack adequate environmental flow protections (Grantham et al. 2014). To avoid harming freshwater habitats in our attempts to protect groundwater, we need to ensure that we leave enough water in rivers.

Functional Flows

A potential resource to guide decision-making around Flood-MAR projects is the California Environmental Flows Framework (CEFF), described in previous posts here, here, and here. CEFF emphasizes the need to consider flows that support ecological functions throughout the year as a foundational principle in water allocation decision-making.

CEFF identifies five functional flow components that support ecological health while allowing for human water use. These include fall pulse flows at the beginning of the wet season, elevated wet season baseflow in the winter and spring, some targeted peak magnitude flows during large storm events, gradual spring recession flows, and the dry season baseflow (Figure 1). The functional flows approach requires that each of the five functional flows be considered when setting flow targets (Yarnell et al. 2015; 2020; Stein et al. 2021).

This approach can help explore potential benefits – and risks – of Flood-MAR. For example, recharge has potential to restore the dry-season baseflow fed by replenished shallow aquifers. Dry-season baseflow helps maintain water quality, cooler temperatures, and critical over-summering habitat for juvenile salmon and other native fish species. Baseflow also is often the only source of water for wetlands, riparian vegetation, and other groundwater-dependent ecosystems.

The CEFF approach can also inform decisions about how much water can be diverted from wet season peak flows for Flood-MAR. For example, in some rivers, peak flows are artificially inflated from urbanization or dam releases. Diverting artificially elevated flows to within their natural range could help to reduce erosion and excessive scouring and reduce the risk of flooding in communities adjacent to streams. In rivers with more natural peak flows, CEFF would suggest protecting flood flows with important ecological functions (for example the 2-, 5-, and 10-year peaks), but capturing water from other high flow events.

CEFF also can help identify potential negative ecological impacts of managed flood recharge. For example, if large volumes of water are diverted for recharge at the wrong time, this could reduce or eliminate peak flow events and reduce the variability and magnitude of the wet-season baseflow. Winter baseflow and peak flow events from storms support important ecosystem functions such as cueing and supporting migration and creating and maintaining habitat for aquatic species. For example, high flows inundate floodplains that provide major rearing and breeding habitats for many native fishes and scour and reshape river channels over time.

Poorly-timed or excessive diversions in the spring or fall could also disrupt the spring recession and fall pulse flow. The spring recession flow redistributes sediment, maintains cool water temperature, and provides migratory and reproductive cues. The gradual reduction in flow improves habitat diversity within the channel and provides time for vegetation and wildlife to prepare for dry season conditions. The fall pulse flow flushes fine sediment from the channel and reconnects the channel at the end of the dry season, improving water quality and cuing the start of migration.

Given the importance of wet-season functional flows, Flood-MAR should be designed to ensure that diversion of wet-season flows:

• avoids altering or removing important cueing flows or impairing the movement of organisms through river networks, particularly migratory species such as salmon and steelhead trout;
• protects the frequency, duration, or extent of downstream floodplain inundation associated with the 2-year, 5-year, and 10-year recurrence interval peak flows;
• maintains sediment transport processes that create habitat for aquatic and riparian species; and
  • is combined with reducing flow alteration for any other altered flow components, such as using recharge to reduce water consumption during the dry season.

In addition, to achieve groundwater sustainability, recharge must not increase consumptive use. Managed aquifer recharge programs should consider how recharged supplies will be managed and include provisions to avoid overexploitation. Without these safeguards, recharged water is unlikely to benefit the environment and could worsen environmental impacts.

Using functional flows to evaluate water available for Flood-MAR

Tools developed through CEFF may be useful for assessing the amount of water available for Flood-MAR. As part of this work, natural functional flow ranges have been modeled for every stream reach in California and can be used to recommend protective flow thresholds for water withdrawals (Grantham et al. 2022).

Figure 2A shows an example functional flow regime under CEFF for a coastal river. With CEFF, high flows would be available for diversion to recharge above the wet-season median flow magnitude for a wet year. A functional flow regime also would recommend that the first one to two 2-, 5-, and 10-year peak flows pass with a natural recession. CEFF would also suggest that the timing of diversion for recharge be restricted to December through March because this window avoids impacts to the spring recession and fall pulse flows. In streams where winter flows are relatively natural and support a community of native species, an additional protective criterion capping diversion could be included at 20% of actual daily flow (Figure 2B). The functional flow regime with a maximum 20% diversion rate protects more wet season variability, which can benefit species that move or occupy temporarily flooded areas such as side channels.

In streams with highly altered channels or impaired water quality, reference ranges may need to be adjusted to consider more realistic channel capacity and baseflows to maintain water temperature. See more discussion in the CEFF technical report, Section B. In addition, some of the “available” water may be allocated to downstream uses, so evaluation of downstream water requirements would be an important part of any analysis.

We can also compare this scenario to the State Water Resources Control Board’s streamlined approach to permitting for Flood-MAR, known as the “90th percentile /20 percent rule” (90/20 rule). Under the 90/20 rule, water is available for diversion to recharge on a given day if instream flow exceeds flow in 90% of years for that calendar day and the diversion will represent less than 20% of instantaneous flow (Figure 2C). The two functional flow regimes allow diversion on more days than the 90/20 rule in most years, but all three usually protect functional flows. In a river with more extensive modifications to wet season flow, the 90/20 rule, which does not consider naturally occurring flows, might allow more diversion than the functional flow regime. Each ruleset limits diversion to days and years with high flows to minimize ecological impact.

The future of flooding

To improve water system resilience, recharge should lessen overdraft rather than expand water use. A focus on functional flows can help minimize the negative ecological consequences of diversions, while allowing diversion for recharge to replenish depleted aquifers. A complete functional flow analysis also would evaluate alteration to the other four functional flow components and seek to improve or maintain functional flows throughout the year.

To ensure meaningful recharge, we also need to continue to develop methods to measure and monitor recharge benefits. Flood-MAR benefits could include higher groundwater levels, increased dry-season baseflow, and a reduction in summertime pumping or diversions. CEFF can help assess these benefits. Without quantification and assessment, it’s difficult to know whether recharge is helping to address groundwater overdraft or simply increasing our reliance on variable surface flows through expanded consumptive use. Quantification of benefits can help adaptively manage recharge.

How can we achieve the promised benefits of Flood-MAR? By treating it as part of a solution to the overdraft we currently face, rather than as a novel source of supply. We have a critical need to improve the resilience of our water supply and our ecosystems, to manage both the variable conditions we’re experiencing now and the projected future under climate change. Reducing groundwater overdraft and enhancing recharge are an important part of the solution, together with efficiency and other demand reduction measures, and by focusing on reducing vulnerability and stabilizing rather than increasing supply, we can move one step closer.

Further reading

• The California Environmental Flows Framework –https://ceff.ucdavis.edu/
• Grantham, T. E., Mount, J., Stein, E. D., and Yarnell, S. M. (2020). Making the Most of Water for the Environment: A Functional Flows Approach for California’s Rivers. San Francisco, CA: Public Policy Institute of California Water Policy Center. https://www.ppic.org/publication/making-the-most-of-water-for-the-environment/
• Yarnell, S., E. Stein, J. Webb, T. Grantham, R. Lusardi, J. Zimmerman, R. Peek, B. Lane, J. Howard, and S. Sandoval-Solis. (2020). A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications. River Research and Applications 36:318–324.

Author affiliation:

Bronwen Stanford is the lead river scientist and Julie Zimmerman is the director of science for The Nature Conservancy’s California water program. Kris Taniguchi-Quan is a senior scientist and Eric Stein is the department head of the biology department at the Southern California Coastal Water Research Project. Ted Grantham is an associate professor of cooperative extension at UC Berkeley. Sarah Yarnell is a research hydrologist at the UC Davis Center for Watershed Sciences. Alyssa Obester is a senior environmental scientist. Jessi Ayers is a research scientist at USGS. Alex Milward is an environmental scientist.

References

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Grantham, T. E., D. M. Carlisle, J. Howard, B. Lane, R. Lusardi, A. Obester, S. Sandoval-Solis, B. Stanford, E. D. Stein, K. T. Taniguchi-Quan, S. M. Yarnell, and J. K. H. Zimmerman. 2022. Modeling functional flows in California’s rivers. Frontiers in Environmental Science 10.

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.

Michel, C. J. 2019. Decoupling outmigration from marine survival indicates outsized influence of streamflow on cohort success for California’s Chinook salmon populations. Canadian Journal of Fisheries and Aquatic Sciences 76:1398–1410.

Mount, J., E. Hanak, K. Baerenklau, V. Butsic, et al. 2018. Managing drought in a changing climate: four essential reforms. Public Policy Institute of California. 

Notch, J., A. McHuron, C. Michel, F. Cordoleani, M. Johnson, M. Henderson, and A. Ammann. 2020. Outmigration survival of wild Chinook salmon smolts through the Sacramento River during historic drought and high water conditions. Environmental Biology of Fishes 103:1–16.

Rohde, M. M., T. Biswas, I. W. Housman, L. S. Campbell, K. R. Klausmeyer, and J. K. Howard. 2021. A machine learning approach to predict groundwater levels in California reveals ecosystems at risk. Frontiers in Earth Science 9.

Stein, E. D., J. Zimmerman, S. M. Yarnell, B. Stanford, B. Lane, K. T. Taniguchi-Quan, A. Obester, T. E. Grantham, R. A. Lusardi, and S. Sandoval-Solis. 2021. The California Environmental Flows Framework: meeting the challenges of developing a large-scale environmental flows program. Frontiers in Environmental Science 9.

Yarnell, S. M., G. E. Petts, J. C. Schmidt, A. A. Whipple, E. E. Beller, C. N. Dahm, P. Goodwin, and J. H. Viers. 2015. Functional flows in modified riverscapes: hydrographs, habitats and opportunities. BioScience 65:963–972.

Yarnell, S. M., E. D. Stein, J. A. Webb, T. Grantham, R. A. Lusardi, J. Zimmerman, R. A. Peek, B. A. Lane, J. Howard, and S. Sandoval-Solis. 2020. A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications. River Research and Applications 36:318–324.