The North Delta Habitat Arc: an Ecosystem Strategy for Saving Fish

Cache Slough sunrise, April 2013. Photo by P.B. Moyle

Cache Slough sunrise, April 2013. Photo by P.B. Moyle

Peter Moyle, John Durand, Amber Manfree.  Center for Watershed Sciences, University of California, Davis.

Delta native fishes are in desperate condition. Over 90% of fish sampled by diverse means belong to non-native species.  Native species such as delta smelt are on a trajectory to extinction.  If we are going to reverse this trend, we need to recreate a functioning estuary. This in turn requires more than a piecemeal collection of restoration projects, but an ecosystem-based plan of action, which we present here.

First, we remind you of some basic realities about the Delta:

  • The Delta is and will continue to be a central node in California water supply system, which requires moving Sacramento River water through the Delta to pumping plants.
  • Upstream diversions prevent a substantial amount of water from reaching the Delta.
  • There will be major changes to the Delta from multiple factors, including sea level rise, earthquakes, climate change, and (perhaps) methods of water export.
  • Areas of the Delta dominated by Sacramento River flows are very different ecologically from those on the San Joaquin side.
  • The Delta is an increasingly hostile place for native fishes because of the combination of large-scale habitat change, alien species, and changed hydrodynamics.
  • The Delta as a whole, but especially the south and central Delta, no longer functions well as part of an estuary, because changes in flow alter the dynamic upstream-downstream gradient of habitat characteristic of estuaries.

Regardless of ‘fixes’ proposed for the present cross-Delta water delivery system, major projects to provide habitat for declining native species are needed.  Many projects are already underway or planned. These are mostly in the north and west Delta where more opportunities are provided by availability of suitable land elevations and fresh water from the Sacramento River.


The Delta, showing the North Delta Habitat Arc.

Here we propose the conceptual basis for a Grand Strategy to create an inter-connected series of habitats, mostly tidal, in this region. In some respects this strategy is already underway, but it lacks a unified conceptual, scientific, institutional, and applied approach.

This Grand Strategy creates an arc of habitats connected by the flows of the Sacramento River.  The upstream end of the arc is the Yolo Bypass, and the arc continues through the Cache-Lindsey Slough-Liberty Island region, down the Sacramento River including Twitchell and Sherman Islands, and into Suisun Marsh (See figure). The Cosumnes River-Stone Lakes area would act as a connected floodplain region.  We refer to this arc the North Delta Habitat Arc but it could perhaps be called the Reconciliation Arc, recognizing the highly altered nature of the habitats, the need for continuous management, and their significant compatibility with farming and other activities.

Here are some of current features and actions occurring in the Arc:

Yolo Bypass.  This is the place where we are learning how farmed floodplains can become major contributors to conservation of fish and wildlife. Future projects are likely to include gates on the Fremont Weir to allow annual flooding on some parts of the Bypass, especially in miniature floodplains along the Toe Drain, on the east side of the Bypass.  Re-establishing a natural connection between Putah Creek and Sacramento River through the Bypass should support re-establishment of runs of salmon and other migratory fish in the creek.  Water flowing through Bypass, even as small pulses, also has potential to be a source of food and nutrients for pelagic fishes in the Delta.

North Delta.  The Lindsey-Cache Slough-Liberty Island area is widely regarded as prime real estate for restoration projects, in part because the natural drainage patterns still exist on the landscape and because of its connections with the Sacramento River.  Examples of on-going projects include the reconnection of historic tidal sloughs to Calhoun Cut, the development of a tidal marsh ‘from scratch’ as mitigation habitat, and Liberty Island Ecological Preserve.

Sacramento River.  The Sacramento River as it flows through the Delta is THE major corridor for fish migration:  four runs of Chinook salmon, steelhead, American shad, striped bass, delta smelt, longfin smelt , splittail, green sturgeon, and white sturgeon.  Maintaining flows and water quality is important for all these species.  It is likely that complex, vegetated edge habitat is very important for juvenile fishes moving downstream and perhaps for spawning of delta and longfin smelt.   The restoration of large tracts of tidal marsh on Twitchell and Sherman Islands is likely to benefit migratory species of both fish and birds, as well as to reverse subsidence and perhaps provide ‘food’ for larval and juvenile fishes through export to main channels.  We also envision using ponds within these islands to support populations of Sacramento perch and other native species.

Suisun Marsh.  Suisun Marsh is connected to the Sacramento River by Montezuma Slough, which has large tidal gates near its upstream end.   The tidal gates regulate salinities in the Marsh, keeping conditions fresher during late summer and fall. The high potential of Suisun Marsh to support native fishes is increasingly being recognized.  New projects are being started or proposed, such as finding ways to manage duck hunting clubs for both fish and ducks, creating tidal habitat that mimics conditions in remaining ‘natural’ tidal sloughs, and making Roaring River Slough into a flow-through system, rather than just a dead-end water delivery system for duck clubs.

These areas each have their own distinctive characteristics and faunas. Collectively, the many projects should be regarded as a large-scale example of reconciliation ecology, where new habitats are created and closely managed by people to meet specific goals. The biota of these new habitats is a mixture of native and non-native species that together form novel ecosystems.

Viewing the Arc as a large inter-connected and reconciled ecosystem should help us to:

  • Manage projects to benefit a full range of life history stages for key species. For example, splittail spawn on floodplains but rear in brackish tidal marsh, so they need the entire system to support their life history.
  • Coordinate management of restoration projects with water project operations.
  • Manage the system in a changing climate: longer droughts, bigger floods, and warmer temperatures.
  • Restore tidal marshes as sources of food for pelagic fishes such as delta smelt.
  • Compare outcomes of different restoration strategies.
  • Assess how tidal marsh restoration projects affect tidal flow in projects, given that total tidal energy is more or less fixed.

We recognize that we are essentially recommending that reconciliation efforts be focused on about one third of the Delta, especially for fishes.  In the Central and South Delta, the realm of subsided, riprap-ringed islands and major pumping plants, it is hard to see much future for native fishes, although fisheries for alien fishes such as largemouth bass will continue to thrive. We will develop these concepts further in future blogs.

Further reading:

Moyle, P. B.; L. R. Brown, J.R. Durand, and J.A. Hobbs. 2016. Delta Smelt: life history and decline of a once-abundant species in the San Francisco EstuarySan Francisco Estuary and Watershed Science, 14(2). jmie_sfews_31667. Retrieved from:

Quiñones, R.M and P.B. Moyle. 2014. Climate change vulnerability of freshwater fishes in the San Francisco Bay Area. San Francisco Estuary and Watershed Science 12(3). doi:

Moyle, P.B., A. D.  Manfree, and P. L. Fiedler. 2014. Suisun Marsh: Ecological History and Possible Futures.  Berkeley: University of California Press.

Hanak, E., J. Lund, J. Durand, W. Fleenor, B. Gray, J. Medellín-Azuara, J. Mount, P. Moyle, C. Phillips, and B. Thompson. 2013. Stress Relief: Prescriptions for a Healthier Delta Ecosystem. San Francisco: Public Policy Institute of California. Available at

Moyle, P.B.  2013 Ten realities for managing the Delta.  California Water Blog. Center for Watershed Sciences, UC Davis. February 26, 2013.

Moyle. P.B. W. Bennett, J. Durand, W.Fleenor, J. Lund, J.Mount, E. Hanak, and B. Gray. 2012. Reconciling wild things with tamed species- a future for native fish species in the Delta. California Water Blog. Center for Watershed Sciences,  June 15, 2012.

Moyle, P. B., W. Bennett, J. Durand, W. Fleenor, B. Gray, E. Hanak, J. Lund, J. Mount. 2012. Where the wild things aren’t: making the Delta a better place for native species. San Francisco: Public Policy Institute of California. 53 pages.

Moyle, P.B. 2011. Reconciliation or extinction- the future of California? California Water Blog. Center for Watershed Sciences, February 8, 2011

Lund, J., E. Hanak, W. Fleenor, W. Bennett, R. Howitt, J. Mount, and P. B. Moyle.  2010. Comparing futures for the Sacramento-San Joaquin Delta. Berkeley: University of California Press. 230 pp.

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7 Responses to The North Delta Habitat Arc: an Ecosystem Strategy for Saving Fish

  1. DWR found that 1.2 MAF of water is required to naturally keep the salt water to the west if DAM and Lock was installed across the straights . BUT, in looking at installing a lock blocking only 1/12 of the flow in both directions can be great. This is clearly not a Dam or Barrier like previously studied. The shipping channel is dredged yearly to keep the water way deep for ships, but this also keeps this shipping channel deep which allows the heavier salty sea water a prime channel to move it’s salty water into the Delta. PPIC studied and reported that 71% of fresh water released from northern dams like Shasta to hold back the salt water intrusion.
    If a Lock system to protect the 3 Benicia bridges (1/12 of the 1 mile span) also prevents 20% of the Salty Sea water intrusion that would all less fresh water needed to keep salty water to the west of Benicia and makes the Delta a fresher water area that supports more life(fish, plants, birds, etc…) The 11/12 of the Benicia span can be left just as it is today.

    It would be great to understand if the 1/12 section for the shipping lock will prevent 10%, 20% or 30% of the salt water intrusion into the Delta? If you know of someone that can run this scenario to give me a more scientific answer, that would be great.

  2. Dan Ray says:

    Sounds good, but:
    1. How would tidal marsh be restored on Twitchell and Sherman Islands, given their subsided, below-s sea level elevations?
    2. How would Delta water quality be maintained if Twitchell and Sherman islands no longer contributed to the 8-island “cork-in-the-bottle” barrier to salinity intrusion?

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