The Sacramento San Joaquin
Delta Crisis

Decline of the Delta


The Sacramento-San Joaquin Delta is located at the confluence of the Sacramento and San Joaquin rivers, and just east of where the rivers enter Suisun Bay. The Delta is part of the Bay-Delta estuary and the larger Bay-Delta ecosystem which extends from Sierra Rivers to the Gulf of the Farallones. Estuaries are areas where fresh water from rivers and streams mixes with saltwater tidal flows, creating nutrient rich brackish waters.

The Delta

Estuaries provide spawning grounds for some fish species, and rearing areas and migratory pathways for others, including salmon. The most productive fishing grounds along the Pacific Coast are typically located offshore of estuaries. Juvenile salmonids rear in estuarine wetland habitat during their downward migrations to the sea. In such habitat they forage for food, find shelter from predators, grow, and build strength as they transition from freshwater to life in the sea.

Our Bay-Delta is the largest estuarine ecosystem along the entire west coast of North and South America. It is considered by many to be California's most important ecosystem. The Delta serves as the hub of California's water supply, making it a vital resource for California's infrastructure and economy. It has become ground-zero in the fight over water allocation in California. The outcome will determine whether the Bay-Delta's fish and wildlife resources, and the economy they support, will be restored or destroyed.

Before major development for land and water use, the historic Bay-Delta landscape consisted of vast areas of brackish and fresh water marshes, intertidal wetlands, and their associated waterways and sloughs. They created a rich and complex ecosystem which supported a great diversity of fish and wildlife. Resident fish species included delta smelt, longfin smelt, Sacramento splittail, Sacramento perch, thicktail chub, and others. Anadromous fish included Chinook and Coho salmon, steelhead, and green and white sturgeon.

The Bay-Delta is in a state of ecological crisis. Some native fish species that were historically abundant are threatened, endangered, or extinct. Coho salmon, Sacramento perch and thicktail chub are no longer found in the Bay-Delta. Populations of Chinook salmon, steelhead, green and white sturgeon, delta smelt, longfin smelt, Sacramento splittail, and other fish have dramatically declined. Concentrations of phytoplankton and zooplankton have dropped sharply, bringing the food chain to the brink of collapse. The migratory pathways have become a deadly gauntlet for salmon and steelhead. Large areas have become dominated by destructive invasive species.

Factors in the Decline


Many factors have contributed to the Delta's decline. A summary follows. The map at this link shows an overview of the modern Delta.

So much fresh water is diverted upstream and in the Delta that what remains is not sufficient to support the needs of fish and wildlife. Average annual freshwater outflows from the Delta to the Bay are only about half of natural unimpaired flows. About 31% of unimpaired flows are diverted upstream before they reach the Delta. Inflows to the Delta from the San Joaquin River are reduced by up to 80% in dry years. The state and federal water projects operate massive pumping facilities in the south Delta. They export about 17% of total freshwater flows. In-Delta diversions take about 4%. Exact percentages vary from year to year depending on rainfall. Sierra winter runoff and spring snowmelt historically provided high winter and spring cold water flows through the Delta. They inundated floodplains, helped transport migrating juvenile salmon through the Delta to the sea, and provided many other benefits to native fish and wildlife. Water management practices have dramatically reduced the ecologically critical winter and spring flows. Winter-spring runoff now gets captured and stored behind dams to be exported in the summer for agricultural irrigation and other uses.

Export pumping distorts natural flow patterns and kills enormous numbers of fish. The Delta's main source of fresh water is the Sacramento River. It contributes about 75-80% in most years. This means most fresh water enters on the north side of the Delta. The state and federal export pumps are located in the south Delta. The need to move large volumes of Sacramento River water to the pumps creates highly altered flow patterns. The pumps redirect net Delta flows in a north-south direction instead of the natural downstream direction from east to west. They pull Sacramento River water through the Delta Cross-Channel and Georgiana Slough, through the central Delta and south toward the pumps. Export pumping causes net reverse flows in the south Delta; water flows upstream to the pumps rather than downstream to the sea. Juvenile salmon get pulled off their migration routes down the Sacramento, San Joaquin and Mokelumne Rivers. Millions of salmon and other fish get pulled into conveyance channels where they are eaten by predators or killed at the pumps. Incomplete counting procedures underestimate the numbers of fish killed, directly and indirectly, by pumping operations. The true numbers are almost certainly in the tens of millions of fish annually. Export pumping also removes organic material, nutrients, phytoplankton and zooplankton which would otherwise support the base of the Delta food chain.

The Bay-Delta is listed under the Federal Clean Water Act as impaired for a variety of toxic contaminants. These include pesticides, selenium, ammonia, mercury, and other pollutants from agricultural, industrial, and urban sources. Inflows to the Delta from the San Joaquin River can be of especially poor quality due to high temperatures, salts, pesticides and other pollutants. Poor water quality in combination with low flows has contributed to declines of Chinook salmon in San Joaquin Basin rivers. The effects of pollution in the Delta are not as well understood. While pollution is always a cause for concern, we are not aware of strong scientific evidence that it is a significant cause of the recent catastrophic declines of many other Delta fish species. There is much stronger evidence linking these declines to increased export pumping and insufficient freshwater flows. Reduced flows also compound the effects of pollution by further concentrating pollutants and causing them to flush out of the Delta more slowly.

Historic Delta waterways created a complex network of rivers, sloughs and dead-end channels connecting to marshes and seasonal floodplains. Inundated marshes and floodplains create high quality habitat for some species. They also enhance the food chain by supplying sediments, organic materials, nutrients, and plankton to adjacent river channels and downstream areas. This "ecosystem fertilization" is another example of how freshwater flows promote fish and wildlife abundance in estuaries. The historic channel network connected vast areas of high quality habitat that included natural flows, abundant food and protective cover.

About 95% of historic wetlands have been removed from the ecosystem. Most of these areas were converted to farmland. Land conversion and water conveyance drove efforts to redesign the Delta's waterways. They were deepened, widened, straightened, armored, confined between levees, and disconnected from floodplains and marshes. Elements which provided habitat structure and protective cover including bank vegetation and fallen trees were removed. Cross-channels were built to connect what were historically disconnected waterways whose separation had helped provide a diverse aquatic environment. These actions altered natural flow routes and created an unnaturally uniform environment. They reduced habitat quantity and quality, and food chain productivity. They eliminated most of the historic channel network and turned what remained into a system of simplified, interconnected, levee-confined conveyance canals designed to maximize movement of fresh water to the pumps.

Compare these maps of historic habitat and habitat today. Most wetlands and channel network are gone. (Historic) (Today)

Compare today's levee confined channels to historic habitat.

Although channel simplification and wetland habitat loss are long term factors in the Delta's decline, they did not cause the recent collapse of salmon and other native fish. Most wetland loss occurred decades ago, long before the recent collapse. However, low flows and increased export pumping amplify the problems by further reducing habitat quantity and quality, further degrading food chain productivity, causing even greater distortion of natural flow patterns, and pulling millions of fish into the conveyance channels where many don't survive.

The Delta's unnatural flow patterns also support invasive predator and competitor species. The Bay-Delta has been labeled "the most invaded estuary on earth". Invasive alien plants in the central and southern Delta include Brazilian waterweed and water hyacinth. They choke waterways, impede flows, increase surface water temperatures, filter sediments and nutrients from the water, reduce planktonic growth, and provide ambush habitat for predatory alien fish. Alien freshwater fish in the central and southern Delta, most of which evolved in warm slow moving water bodies in the southeastern United States, include largemouth bass, bluegill sunfish, and white catfish. Aliens prey upon and drive out juvenile salmon and other native fish. Experts believe the numbers of fish eaten by predators in channels leading to the pumps are even greater than those killed directly at the pumps.

Native Delta fish species evolved under highly variable flow and water quality conditions. Water management practices and the conversion of historic waterways into conveyance canals have reduced natural variability and created highly altered conditions. The interconnected canals in combination with export pumping and tidal forces maximize water movement across large areas. This causes water from different areas to mix rapidly, reducing variability and homogenizing water quality. Natural seasonal variations and seaward gradients in temperature, turbidity, salinity and flow have been altered and reduced. Water conditions are more warm, clear, uniform and stable than they were historically. This favors a narrower group of alien aquatic species which prefer these stable, low flow conditions and which are more commonly associated with temperate freshwater lakes.

Salinity standards require enough freshwater outflows through the Delta to the Bay to keep salt water out of the Delta interior and away from the pumps. The standards allow water management agencies to eliminate high winter-spring flows during wet years and withold the water for summer exports and other uses instead. Fresh water outflows are artificially stabilized, or "flat-lined", as releases from upstream dams are managed to provide just enough outflows to meet the standards. High winter-spring cold water flows through the Delta to the Bay have been dramatically reduced and replaced by warmer, clearer summer flows from the Sacramento River to the pumps. Reduced fluctuations in salinity favor invasive freshwater fish to the detriment of native fish.

The steep-sided, levee-confined channels provide very little food or protective cover for native fish. Export pumping pulls millions of native fish into the channels where they become food for invasive predators. Increased water clarity makes it easier for predators to see and catch their prey. Warm water temperatures and lack of food cause juvenile salmon to become stressed and less able to escape from predators. These conditions provide competitive advantages to predatory warm-water fish adapted to lake environments over natives adapted to the more variable historic Delta environment. Restoring more natural flow and habitat conditions could help tip the balance back in favor of salmon and other desirable fish.

The above conditions have also helped freshwater Asian clams reach extremely high densities in some areas of the central and southern Delta. These voracious filter feeders disrupt the food chain and degrade habitat for native fish by consuming vast quantities of phytoplankton in areas where they dominate. Overbite clams, also from Asia, have invaded large areas in the western Delta and Suisun Bay. Historic high winter-spring flows made these areas seasonally fresh. Today's artificially stabilized conditions keep the western Delta and Suisun Bay brackish most of the time. These conditions favor overbite clams which do well in brackish water but not freshwater. Higher and more variable freshwater flows could help control the spread of these destructive species.

Ideally, all of the above stressors should be reduced or eliminated. It's not possible to recover all historic habitat or eliminate all invasive species. But, damage caused by increased export pumping and low freshwater flows can be greatly reduced by changing water management practices. There is strong scientific evidence that low flows and altered flow patterns are a major contributor to the ongoing collapse of salmon and other fish and that flows must be restored if we are to turn the collapse around. Restored flows alone can't fix all of the Delta's problems. Habitat restoration and other improvements are needed. However, they can't be expected to recover the Delta without adequate freshwater flows. Flows are the foundation for recovery.

For more information on how insufficient freshwater flows is killing the Bay-Delta ecosystem, see the Bay Institute's report, Gone with the Flow.

For more information on how Delta export pumping kills millions of fish each year, see the Bay Institute's report, Collateral Damage.

Delta Exports and Flow Recommendations


Water diversions for in-Delta uses have remained fairly steady at slightly over 1 million acre-feet (MAF) per year. However, exports by state and federal water projects have increased dramatically for several decades. Five year averages increased from less than 3MAF in 1968-72 to more than 6MAF in 2003-2007. Declines of salmon and other fish accelerated sharply during these years. This is no coincidence. Scientists and fishery advocates have long known that the Delta's ecosystem and fish populations have suffered because too much fresh water is diverted. A major barrier to progress has been that there was no credible answer to the question; how much freshwater flow do the Bay-Delta's fish need? San Joaquin Valley irrigators have demanded more and more water even as fish populations crashed and the salmon industry shut down. Meanwhile, flow needs for the Delta were left undefined and indeed suppressed. Finally, this has changed.

In August of 2010, the State Water Board released a report identifying flows needed to protect public trust resources and water quality in the Delta. The Water Board found that much more water should flow through the Delta than does today. The report was mandated by the state legislature as part of the Sacramento-San Joaquin Delta Reform Act of 2009. These flows are intended to restore fish populations and not simply to prevent extinctions. The scope of the report was to quantify flow needs for the Delta but not to balance the Delta's needs against other needs for water. The report is not legally binding but is intended to inform the Bay Delta Conservation Plan (BDCP) process, the Delta Stewardship Council's Delta management plan, and future State Board rulings that could improve freshwater flows through the Delta.

The report says, "Restoring environmental variability in the Delta is fundamentally inconsistent with continuing to move large volumes of water through the Delta for export", and that current Delta water policies have been "disastrous for desirable fish". The report recommends that, ideally, about 75 percent of all fresh water runnoff in the Delta's watershed should flow through the Delta and out to the Bay. Today, about 50 percent flows through the Delta on average with lower percentages in some years. In rough terms, upriver and in-Delta water use would need to be cut by half to meet the 75 percent target. Four specific recommendations follow.

  • 75% of natural runoff in the Sacramento River should flow into the Delta in the winter and spring versus about 50% on average today.
  • 60% of natural runoff in the San Joaquin River should flow into the Delta in the winter and spring versus about 40% in wet years and 20% in dry years today.
  • 75% of natural flows into the Delta should flow through the Delta and out to the bay in the winter and spring versus about 50% in on average today.
  • Sufficient outflows should flow through the Delta during the fall to maintain positive flows or low reverse flows in south Delta channels in most years. Compare this to recent reverse flows up to -8,000 cubic feet per second.

These flows can't be achieved by changing Delta pumping operations alone. In-Delta and upriver operations would both need to change. It will be critical to balance Delta flow needs against upriver needs. These flows would require higher releases from upstream dams in the winter and spring. Releases must be managed to conserve the supply of cold water which salmon and steelhead need for adult holding, spawning, egg incubation and juvenile rearing in the upper river reaches. These potentially conflicting needs must be reconciled before Delta flow standards can be finalized. The report can be downloaded here.

Delta Conveyance


Water4Fish is not necessarily opposed to a new conveyance system if it is actually designed and operated to protect the Delta and its fisheries. We don't believe it's feasible to stop all Delta water exports. Water is needed for urban, industrial, and agricultural uses. The design and operation of today's system, in combination with upstream management, have caused or contributed to a disastrous set of problems. These include inadequate freshwater flows, altered flow patterns and reverse flows, salmon migration disruptions, crashing populations of salmon and other desirable fish, and the spread of destructive invasive species. We would be willing to consider a new system if it offers enough improvement over the current system.

Some scientists have raised other concerns about today's conveyance system. These include its reliance on aging Delta levees and the location of the fresh water intakes in the south Delta. They warn a time may come when the system will no longer provide a reliable water supply. They predict that sea level rise is likely to move salt water into the western and southern Delta, close to the pumps. Climate change may also cause more frequent and severe floods. Severe high water events in combination with land subsidence in Delta islands would put increased pressure on the levees and create higher risks of levee failures. Some Delta stakeholders have countered that better maintenance and repair can reduce the risks of levee failures.

This map shows the Delta levees.

This map shows Delta land subsidence.

Scientists also warn that many levees could fail catastrophically in the event of a strong earthquake near the Delta. It may not be economically feasible to strengthen many levees to no-fault seismic standards. Some Delta islands have subsided to 15 feet or more below sea level. Multiple levee failures could cause water to rush in and fill the islands. If this happens during a period of low to moderate Delta inflows, it could pull enough salt water into the Delta interior to make water there too salty for drinking and agriculture. That could shut off water deliveries. The damage may or may not be quickly repairable depending on extent and severity. Water supply disruption costs combined with costs to repair multiple broken levees and flooded islands could be in the billions of dollars. Some people believe these risks are greatly exaggerated. However, the U.S. Geological Survey reported that seismic risks in the Delta are probably even greater than previously believed. A discussion of these risks is available here.

The purpose of any new system should be to meet the co-equal goals of restoring the ecosystem and increasing reliability of the water supply. Increasing reliability means reducing the risks of water supply disruption from regulatory requirements, earthquakes, floods and sea level rise. It does not mean increasing water export volumes. In fact, increasing the volume of water that exporters expect will result in a less reliable supply during years when rainfall limitations cause available volumes to be lower than expected volumes. Any new system should comply with State policy to reduce reliance on Delta exports. It should allow higher freshwater flows and more natural flow patterns than today's system. It should uphold all applicable protections under state and federal ESA, Clean Water Act, and other environmental protection laws. These changes, together with habitat restoration and other improvements, could help tip the balance back in favor of salmon and other desirable fish. Finally, the benefits of any new system should be very carefully weighed against the costs.

We are not prepared to take a position in favor of any particular conveyance option at this time. It would be premature to take such a position before specific proposals become available and are thoroughly and credibly analyzed. We are strongly opposed to BDCP's proposals to date and have serious doubts that BDCP will ever develop an acceptable solution. The decision to proceed with any new system should be driven by sound science and not by the demands of water contractors. It should be based on which option can best meet the co-equal goals of the Delta Reform Act.

The Bay Institute is at the forefront in the fight to protect and restore Sierra Rivers and the Bay-Delta. For more information and to support Bay Institute, go to