While everyone agrees the Delta is no longer an optimal environment for its native species, parties continue to disagree on its root cause.  The estuary is impacted by a variety of stressors that have made the estuary unreliable for both fish and water supply.

Read below for further details on each stressor.

Few issues in the Delta are as clear cut as predation. Larger predator species eat smaller fish with potential devastating impacts on native endangered species such as salmon and smelt. Nonnative species pose a particularly significant predation threat in the estuary. Many of these predators were planted in the Delta for sport and recreational fishing purposes, with little concern for the native species they now endanger such as salmon, delta smelt and steelhead. Exacerbating the problem, it has long been the State’s misguided policy to protect and maintain the populations of these predators through the use of size and bag limits. Fish stocking programs have also been utilized in the past to increase the adult populations of these voracious feeders. Many species that are nonnative to the Delta have direct or indirect impacts on native threatened species, which greatly reduces survival of native fishes. Striped bass represent a direct predatory threat to the delta smelt and salmon and yet are protected by an ongoing California Department of Fish and Game program that maintains the population at artificially high levels to the detriment of native species. Until 1992, the Department restocked striped bass as part of an active population management program.
Coalition Efforts
  • The Coalition filed a lawsuit against the California Department of Fish and Wildlife (DFW) for violating the ESA through its enforcement of State sport fishing regulations. The lawsuit was successfully settled requiring DFW to collaborate with the National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (FWS) to develop a joint regulatory proposal addressing the impacts of sport-fishing regulations on listed species. However, the California Fish and Game Commission decline to accept the recommendation at that time.
  • Since then, the Coalition has successfully worked with the Commission to update their outdated striped bass policies and institute new Delta Fisheries Management Policies that appropriately prioritize the management of native endangered fish in the Delta.
Other States
Washington and Oregon are both home to endangered Columbia River Salmon populations whose conditions have been exacerbated by drought conditions and non-native predator species.
  • In 2019 the Washington Department of Fish and Wildlife (WDFW) removed size and bag limits on non-native bass and walleye in the state.
  • The decision came in response to legislation aimed at increasing chinook survival in hopes of helping struggling orca populations in the Puget Sound.
  • In 2015 the Oregon Department of Fish and Wildlife removed bag limits for warmwater fish (including bass and walleye) in the Columbia, John Day and Umpqua rivers.
According to the California Department of Water Resources, climate change is already having an impact on California’s water resources and the Sacramento-San Joaquin Delta. Existing climate change models predict that warmer temperatures, changing patterns of precipitation and run-off and rising sea levels will profoundly affect the Delta ecosystem and ecology.   The Public Policy Institute of California  points out that climate change has particularly serious implications for the Delta’s weakened levee system. Climate change is expected to increase flood risks as sea levels rise.   Snowpack is a key component to California’s water supply system. While rains may fill reservoir, rivers, and streams, these supplies are often diminished during warmer months. Just as spring months begin to increase water usage, snowpack begins to melt refilling much of the reservoirs’ supply. Without snowpack, the state’s water system will require significant changes. Additionally, if rain fall significantly increases, these additional flows will further increase flood risk.   The Public Policy Institute of California put out an additional report discussing California’s future in relation to climate change. While also discussing the risk of flooding, the reports adds climate change effects are likely to include more frequent droughts and higher temperatures causing more rain rather than snow.   As California begins to see a changing climate, adaptations and infrastructure upgrades will be needed. The Delta should be a priority for many of these improves in order to protect residents, businesses and the state’s main water supply hub.
According to a 2014 State Water Resources Control Board (SWRCB) report, there are more than 3,000 known in-Delta water rights and claims. However, evidence suggests that there are hundreds of additional water users in the Delta illegally diverting water. In a 2004 U.S. Fish and Wildlife Service delta smelt 5 year review, it was estimated that local in-Delta diverters export up to 5,000 cubic feet per second (cfs) from the Delta – or almost half as much as the combined federal and state pumping plants maximum export rate of up to 11,000 cfs. Unlike the Central Valley Project (CVP) and State Water Project (SWP), pumping operations at these local diversions are not regulated to limit impacts on endangered species.   The number of agricultural in-Delta diversions has expanded over the past decade and therefore, the rate of unscreened and unregulated diversions has likely increased. Agencies and experts, including the U.S. fish and Wildlife Service, acknowledge that unscreened in-Delta diversions may impact the delta smelt through entrainment and hydrodynamic influence. However, State and federal regulators have expended little or no effort to date to determine the effects of these unscreened pumps, or to regulate or monitor these diversions in order to slow the decline of endangered species.
Poor oceanic feeding conditions and commercial fishing have been identified as key causes of the collapse of Sacramento River fall run Chinook salmon.   According to the National Marine Fisheries Service, immediately prior to the sharp salmon decline in 2007, rising temperatures in the Pacific Ocean depleted much needed nutrients. Salmon that spend most of their life in ocean waters can be decimated by the lack of food available as a result of changing ocean conditions. As a result, oceanic conditions can have dramatic impacts on the salmon runs in the Delta from year to year.   Sacramento River fall Chinook (not listed per the Endangered Species Act) has traditionally been considered the primary salmon stock supporting California ocean fisheries, historically comprising 80-95 percent of the salmon catch. In 2003 at the height of commercial salmon fishing in California, Chinook Salmon ocean harvest totaled 6,391,621 pounds. (In 2011, only 990,977 Chinook Salmon were harvested.) This dramatically reduces the number of salmon returning upriver to spawn and increased the prevalence of hatchery born salmon released to the wild.   In comparison, a study by the Department of Water Resources found that only 0.4 percent of Delta salmon are lost directly at the Delta pumps.   The winter-run Chinook has particularly struggled. Unlike the popularly fished fall-run and spring-run, the winter-run is endangered. While there are restrictions on the taking of the endangered winter-run, it can be nearly impossible for fishermen to distinguish between winter-run and fall-run at the time of harvest. This leads to the inevitability that as more fall-run are harvested, increasing numbers of already scarce winter-run will be lost as well.   Fishbio reported that the Pacific Fisheries Management Council (PFMC) uses an outdated and highly inaccurate model to predict salmon abundance on the West Coast. The Salmon Technical Team uses data on the number of fall-run Chinook jacks (two-year old fish) that returned to the Sacramento River the previous fall to calculate a forecasted index of abundance, called the Sacramento Index (SI). The SI is the number of adult fish projected to be available for ocean harvest or that will escape to the Central Valley. PFMC uses the SI to set annual fishing regulations.   Since 2005, PFMC has overestimated the SI nine times. In 2012 and 2014, the Salmon Technical Team attempted to develop more accurate forecasting methods. Each new forecast was closer to actual numbers, but still inaccurate.   The Salmon Technical Team expressed concern that setting high harvest limits for fall-run Chinook based on overly optimistic estimates may increase the bycatch of endangered Sacramento River Winter-run Chinook salmon in the fishery.
California’s two main water supply projects, the Federal Central Valley Project (CVP) and State Water Project (SWP) depend on the Delta to deliver water for 25 million residents and thousands of farms and businesses. While activists single out these pumps as the cause of all of the Delta’s problems, increasing evidence suggests that these water pumping projects are only one of many factors and human activities impacting the estuary.   Regulatory decisions continue to impose severe pumping restrictions on the state’s water delivery system. These decisions are shortsighted because they fail to consider other critical factors or “stressors” impacting the estuary, such as those outlined on this site, to address the Delta crisis.
The effects of human development on the Delta ecosystem are numerous. Local stakeholders in the Delta never fail to highlight the impacts of water pumping operations, but their narrow focus on water exports ignores the pollution they are putting into the estuary and its effects on water quality and wildlife.   Municipal wastewater is directly discharged to Delta waterways from more than 300 municipal sources. Many of these municipal discharges are located in the heart of the Delta, where they release directly into the critical habitat of endangered fish species. These discharges lead to increased pollution, including toxic contaminants such as ammonia, heavy metals, and even pharmaceuticals. As population continues to increase in the region, so will wastewater discharges and their impacts on the estuary.   Consider the following:
  • Every day, up to one billion gallons of partially treated sewage is flushed into the Sacramento San Joaquin Delta.
  • There are at least 52 wastewater discharge sites in the Delta and an additional 25 stormwater discharge sites, each contributing to the pollution of the estuary.
  • A 2008 investigation by the Associated Press revealed the presence of pharmaceuticals in the drinking water of major metropolitan areas. Scientific evidence suggests even small amounts of such substances – including estrogen, antibiotics and heart medications – may adversely affect habitat and fish species. A 2014 study detected concentrations of pharmaceuticals, including carbamazepine, fluoxetine, and trimethoprim, near main Delta wastewater facilities in concentrations that could be chronic to aquatic organisms within the Delta.
  • As a result of Coalition efforts, Sacramento Regional Sanitation District is in the process of updating their wastewater treatment facilities.
  In addition, more than 150 commercial operations, such as mining and other industrial facilities are currently permitted to discharge processed wastewater in and upstream of the Delta. These facilities release as much as 5 million gallons of wastewater each day and have a significant impact on delta water quality, the ecosystem and its fisheries. Industrial materials such as fuel, oil and debris are carried by storm runoff from these facilities into the Delta water ways.   Thousands of abandoned mines also litter the California landscape. Many of these mines are in the Sierra foothills and discharge harmful chemicals such as mercury, chromium, cyanide and asbestos that can pollute drinking water and harm fish and habitat. Runoff from these mines continues to contaminate Delta watersheds and downstream environments contributing to unsafe mercury levels in fish.   But little progress has been made in doing so.   The U.S. Department of Transportation Maritime Administration (MARAD) was found by a federal judge to be illegally polluting and storing hazardous waste in the San Francisco Bay. MARAD is in charge of decaying naval vessels stored in Suisun Bay, which are discharging toxic heavy metals into the waters.   An estimated 20 tons of heavy metals including lead, zinc, copper and cadmium have fallen, blown or washed off the obsolete ships, according to the Federal government’s own analysis. If not cleaned up, they would have shed an additional 50 tons into Suisun Bay.   Under the court settlement MARAD must clean and remove all of the obsolete ships from the Suisun Bay by September 2017. MARAD’s September 30, 2015 update states that MARAD has currently removed 60 non-retention vessels from the bay.   Sources: Sacramento Bee, Associated Press *Information related to the Major NPDES dischargers in the Sacramento/San Joaquin Delta Watershed was retrieved from the California Integrated Water Quality System Project (CIWQS) Regulated Facilities Report available on the website of the State Water Resources Control Board as well as the respective NPDES permits issued to each facility.
It is widely accepted that 95 percent of the Delta’s historic tidal marsh habitat was lost with the development of the Delta’s complex levee system.   Development and increasing demand on Delta resources has a profound impact on natural habitat and continues to have lasting effects today. This increase in human activity has clearly accelerated natural changes in the Delta and will continue to increase pressure on the estuary in the future. With only 5 percent of native habitat remaining, native fish and wildlife populations are struggling.   Urban growth in and around the region in particular can have dramatic effects on the estuary. Not only is habitat altered to accommodate growing communities, but the quality of that habitat is polluted as populations in the region increase.   Higher populations lead to higher pollution through storm water runoff of toxic materials, and municipal waste water and industrial discharges are flushed to the estuary by the growing communities and cities in the region.
The Delta is considered one of the most invaded estuaries in the world.   More than 250 alien aquatic and plant species have impacted the Delta and at least 185 of these species have gained a foothold and are currently inhabiting – and altering – the Delta’s ecosystem. Invasive species represent at least 95 percent of the total biomass in the Delta. New invasive species will continue to arrive. Combined, these invasive species have created an environment uniquely hostile to native fishes.
Predator Fish 
Species such as largemouth bass and striped bass, not only directly consume native species, they also compete with juvenile salmon and delta smelt for food. Of the 40 fish species now residing in the Delta, 28 are non-native. Visit our Striped Bass and Predation pages and read Delta Watch for additional information of non-native fish predation.
Asian Clams (Corbula Amurensis)
Asian have significantly reduced the abundance of plankton, the base of the Delta aquatic food supply and may affect the feeding efficiency and growth of delta smelt larvae. These voracious eaters of plankton have altered entire food webs, harming smelt, salmon and other native Delta species.
Water Hyacinth
Water Hyacinth is an extremely prolific aquatic invasive plant that can double in size every 10 days in hot weather and can quickly become a dense floating mat of vegetation up to 6 feet thick. Mats can attach to structures in the water, limiting access to boats, reducing swimming and fishing areas, and restricting water flow.   From an ecological perspective, water hyacinth can be very damaging to water quality by blocking photosynthesis. Without this basic function, other plants in the ecosystem are unable to add oxygen to the water, reducing other aquatic life such as fish and other plants. Further, water hyacinth can limit biological diversity by restricting other species of plants and blocking access to water for fish and wildlife or eliminating plants these organisms depend on for shelter and nesting.   The hyacinth has a strong hold on the Delta and is now believed to be impossible to eradicate.
Due to both discharges from storm drains and natural run-off to rivers and streams, a number of cities within and up stream of the Delta release hundreds of thousands of gallons of water containing contaminants and toxic chemicals each day.   According to the Center for Biological Diversity, both delta smelt and the plankton on which it feeds are suffering direct mortality or impairment from the presence of toxic substances in the water.   Pyrethroids, among the most widely used home pesticides, are winding up in the Delta at toxic levels, and endangering the food supply of fish and other aquatic animals, according to a new study by researchers at the University of California, Berkeley. Pyrethroids have been around for decades, but their use skyrocketed after 2004, when other home-use pesticides were banned.   Pyrethroid insecticides have been widely found in residential run-off and in the outflow from sewage treatment plants in the Sacramento area. The insecticide is being increasingly found in the San Joaquin River and a 20-mile stretch of the American River – traditionally considered to be one of the most pristine rivers in the region.   Additionally, salinity, herbicides, pesticides, and other toxic chemicals and pollutants from upstream and in-delta farming operation directly impact delta smelt, salmon and other endangered fish and their ecosystem. According to the Center for Biological Diversity (CBD), “…all life stages of delta smelt are at least periodically exposed to lethal or sub-lethal concentrations of herbicides and pesticides…”   According to CBD, both the smelt and the plankton on which the endangered fish feeds are suffering direct mortality or impairment from the presence of toxic substances in the water.   Local communities continue to discharge millions of gallons of treated sewage into the Delta each day. These discharges are believed to have a significant impact on Delta Smelt and other threatened and endangered species.