Peter Moyle, Professor of Fish Biology, University of California-Davis

The Delta and Suisun Marsh were once part of a continuous, enormously productive aquatic ecosystem that supported dense populations of fish from Sacramento perch to salmon, huge flocks of wintering waterfowl, and concentrations of mammals from beaver to tule elk. This amazing ecosystem is gone and cannot be brought back.

The once vast marshes have been turned into farmland and cities, protected by a complex system of levees. The patchy remnants of the original ecosystem are disappearing fast, as more and more native plants and animals become extinct or endangered. In their place, hundreds of alien species thrive in the altered conditions—crabs, clams, worms and fish from all over the world.

We have a choice. We can let the ecosystem continue to slide towards being a mess of alien species that live in unsavory water flowing through un-natural pathways, OR we can take charge and create a new ecosystem that contains the elements we want. Those elements include native species and clean water that flows in more natural patterns, creating a better environment for fish and people.

The State Water Resources Control Board recently supported this concept by recommending that much more fresh water flow through the estuary to the ocean to create a sustainable estuarine ecosystem. More water is only part of the recovery picture, however, because the flows must be managed in new ways and flow through restored habitats. The historical ecosystem can be used only as a model for the new system, mainly to identify conditions that favor remnant native species and have other desirable features. But the new ecosystem will be quite different in its locations, its biota, and how it works.

High variability in environmental conditions in both space and time once made the upper San Francisco Estuary highly productive for native biota, so variability is clearly a key concept for our new ecosystem (Moyle, et al. 2010). Achieving a variable, more complex estuary requires policies that create the following conditions:

(1) Internal Delta flows that create a tidally-mixed, upstream-downstream gradient in water quality, with minimal cross-Delta flows. At times much of the water in the present Delta flows towards the big export pumps in the South Delta. Fish trying to migrate upstream or downstream find this very confusing, often lethally so.

(2) Slough networks with more natural channel geometry and less diked, rip-rapped channel habitat.

(3) More tidal marsh habitat, including shallow (1-2 m) sub-tidal areas, in both fresh and brackish zones of the estuary.

(4) Large expanses of low salinity (1-4 ppt) open water habitat in the Delta.

(5) A hydrodynamic regime where salinities in the upper estuary range from near-fresh to 8-10 ppt periodically to discourage alien species and favor desirable species.

(6) Species-specific actions that reduce abundance of non-native species and increase abundance of desirable species, such as active removal of undesirable clams and vegetation.

(7) Abundant annual floodplain habitat, with additional large areas that flood in less frequent wet years.

(8) Treating the estuary as one inter-connected ecosystem, recognizing that changes in one part of the system will likely effect the other parts.

These habitat actions collectively provide a realistic, if experimental, approach to improving the ability of the estuary to benefit desirable species. Some of these goals are likely to be achieved without deliberate action as the result of sea level rise, climate change, and failure of unsustainable levees in some parts of the Delta. But in the near term, habitat, flow restoration and export reduction projects can allow creation of a more variable and more productive ecosystem than now exists, while accommodating irreversible changes to the system.

Further Reading:

Moyle, P.B., J.R. Lund, W. Bennett and W. Fleenor (2010), Habitat Variability and Complexity in the Upper San Francisco Estuary, San Francisco Estuary and Watershed Science 8(3).

Cunningham, L. (2010), A State of Change: Forgotten Landscapes of California, Heyday Books, Berkeley.