California News Richardson Bay Audubon Center

Water Demand and Our Estuary

The Cost of Reduced Flows to Estuarine Ecosystems
A Great Egret in the San Francisco Bay Estuary
Kate Brewster, Community Conservation Fellow
By Kate Brewster
Community Conservation Fellow, Richardson Bay Audubon Center & Sanctuary (She/Her)
Published October 06, 2026
This article is from Audubon California . Find Audubon near you here.

This summer, as wildfires rip across North America, drought conditions continue across the Western US, and critical freshwater reservoirs draw lower and lower, water is on many of our minds. The Colorado River has been the latest subject of contention concerning water in the West. Negotiations for rights to the Colorado River’s water supply have been locked for months and with no obvious resolution in sight, the federal government has stepped in to propose a plan imposing stricter regulations on water usage which  may not appease any of the seven states which use the river. The plan also includes a chance for renegotiation every two years, which could make things even more convoluted. This and other similar battles between states for natural resources offer a glimpse into the government’s role in navigating a drastically different climate, and California is poised to experience a myriad of climate related stressors.  


California is probably the most hydrologically altered state in the US, and the web of state and federal laws governing its water is just as complex. Our Mediterranean climate, which delivers warm, dry summers and cool, wet winters, coupled with the diversity in landscape and climate across the state, make it so. Most of California’s precipitation falls in the northern half of the state, while most of its population lives in the Southern half of the state. Water has been sent impressive distances across California to irrigate its vast agricultural lands and hydrate its growing cities. 


Lake Powell and Lake Mead, the two reservoirs along the Colorado River, were created to provide hydropower and freshwater for millions of people, but after almost two decades of consistent drought, these lakes have fallen to below 30% of their capacity. Lake Powell’s water levels are expected to drop too low to be drawn by March 2027. As the river yields less and less water, state governments are searching for the best way to divide the dwindling returns. The Colorado River is drawn by seven states, and its water reaches about forty million people and 5.5 million acres of cropland. The main groups that have rights to the river are cities, agrobusinesses, and indigenous communities. Reaching an agreement between the many groups who rely on the river will likely have winners and losers, or perhaps more accurately, losers and bigger losers; all stakeholders will need to relinquish some water. Long term management may require not only reductions by everyone, but also a restructuring of industry in the Southwest. But one side less represented in these conversations is the side of the estuarine and riverine species which depend upon the rivers, delta, and estuary. Wildlife and the environment don’t have legal rights, but they are mentioned in California Fish and Game Code 5937, which requires sufficient water “…to pass over, around and through dams to keep fish in good condition.” This ruling is vague and scarcely enforced. 


The Colorado River once emptied into a rich Delta ecosystem. That delta has been dry for decades now, as the Colorado River has not reached its historic terminus, the Sea of Cortex, in over 30 years. Further north, in the Bay Area and Central Valley, the San Francisco Bay Delta and Estuary, a crucial habitat and migration corridor, faces similar issues to the Colorado of declining water quality and increasing water demand, and this area is also the subject of intense review by legislators. The Delta, which is formed at the juncture of the San Joaquin and Sacramento Rivers, is instrumental to California’s water systems, but it plays an equally critical role as a habitat for many endemic, threatened, or endangered species and a migration corridor for many more. The delta flows into San Francisco Bay, the largest estuary on the West Coast and a critical habitat. This habitat has been significantly altered: shorelines have been armored, vast areas of tidal marshes converted to agricultural land, and freshwater flows reduced. All of these changes make the estuary more volatile, and its species more sensitive. While water demand and its strain on agriculture and cities is heavily discussed, these demands also impact our estuaries and other aquatic habitats, which in turn impact our waterbirds and shorebirds. Even the unbalancing of a single population can have cascading impacts on the entire ecosystem through prey, predator, and competitive interactions. 

The Sacramento Delta

The Sacramento Delta, the only inland delta in the United States, is technically backwards: where most deltas widen as they approach the sea, the wide edge of the Sacramento Delta is at the point of convergence between the two rivers, and these waters enter the estuary through a narrow channel. The dynamics of this delta are likewise unique and independent from other deltas in the United States: it is simultaneously tidal and fresh. Its freshwater is sourced from the snowmelt off the high Sierras, which flows into mountain tributaries that join the San Joaquin and Sacramento Rivers. The freshwater from the delta and saltwater from the Pacific Ocean meet and mix to create the brackish waters of the San Francisco Bay Estuary, and the delta and the estuary comprise two separate but linked ecosystems. The freshwater that enters the delta is also a crucial water resource for California: the southern Delta exports water to more than 25 million people and 3 million acres of irrigated farmland in the Bay Area, the San Joaquin Valley, and Southern California. Humans are a part of the bay and delta ecosystems and we have modified our watersheds to suit the needs of our communities, food systems, and infrastructure, but these modifications do not always suit the broader ecosystem. Developments along wetlands and floodplains have led to the loss of 80% of historical tidal marshes in San Francisco Bay. With the frequent alteration and degradation of essential habitat in this area, it becomes even more essential to protect the connectivity of habitat we still have. 


Where Does Water Diverted from the Delta Go?

Two of the main recipients of the delta diversions are known as the State Water Project and the Central Valley Project, and both use the water for farm and city water supplies, hydropower, and flood diversions. The State Water Project (SWP) transfers water from the Delta to the Bay Area, Southern California, and the Central Coast through 21 dams and over 700 miles of aqueducts and pipelines, to support city water supplies. The Central Valley Project (CVP) also moves water south from the Delta, but its recipients are mostly agrobusinesses. More than 80 percent of California’s developed water (water obtained through reservoirs and groundwater pumping) goes towards agribusinesses. 


This Delta is crucial to both Californians and California native species, and balancing these roles is a mounting challenge for legislators. Much of the Delta’s inflows have been dammed and diverted either to support agriculture, hydropower, and drinking water supplies, or to address flooding concerns. Diverting the Sacramento and San Joaquin Rivers changes the salinity, pH, nutrient availability, and temperature of the water, which affects the health of the plants which populate the estuary, and this in turn changes the quality of habitat for the many organisms which call the estuary home. High flows and floods are essential habitat for juvenile fish, but diversions limit these high flows and provide artificial drought conditions in the estuary. 


The San Joaquin and the Sacramento River have been the subject of recent legal discussions, as the current Bay Delta Conservation Plan has not been updated in over a decade. The newest plans for the Bay Delta affect the way freshwater is parceled for cities, agriculture, hydropower, and indigenous use, and they are intended to balance the needs of the delta ecosystem with the needs of communities and industries. However, these revisions to the Bay Delta Plan are known collectively as the “voluntary agreements,” because instead of imposing data driven water limits for farming districts, the plan relies on small willing sacrifices from major water users to instead flow towards the estuary. Local tribes, environmental interest groups, and fishing communities have criticized this plan for the amount of leeway given to wealthy interest groups, and the lack of oversight towards protecting the Bay Delta. The ecological argument for water may seem less pressing than the agricultural and drinking water arguments. But to understand why freshwater flows are so important to California’s fish, birds, and plants, let’s explore the estuary itself, and its many critical habitats, and inhabitants.  


The San Francisco Bay Estuary

An estuary is the ecosystem formed where freshwater and salt water meet, and the diversity of habitat that exists in and around estuaries make them one of the most important ecosystems in the world, teeming with plant and animal life, and serving as a nursery for fish, birds, crabs, mammals, and many types of invertebrates. More than 120 species of fish and over 30 species of waterfowl live or migrate within the San Francisco Bay Estuary. Over 300,000 shorebirds rest and refuel on their migratory journeys in the mudflats, salt marshes, and saline ponds of the San Francisco Bay each winter. We can think of estuaries as a precarious balancing act, constantly ebbing, flowing, and receiving constant feedback from outside influences. The health of all parts of the system- rivers, sediments, wildlife, and people- are intertwined. The diversity of habitat available in the estuary is threatened by a myriad of issues including pollution, shoreline development, warming, and drought, and the loss of one habitat chips away at the armor of the entire ecosystem, leaving its species more vulnerable to climate change and other threats. 


The reduction of flows from the Delta is not the only threat to native fish species related to water use: the timing of flows is also changed by these diversions. Natural flows typically peak in winter and spring due to snowmelt, and fall to low levels in the fall. In the managed water system, flows are higher in summer and early fall, but diversions cause the spring peak to disappear in most years, and inconveniently the flows from February to June are most critical for native fisheries. Further down the estuary, eelgrass meadows- some of the most prolific habitats for fish and birds- are also endangered by the loss of freshwater flows. 


Eelgrass Ecosystems

On any given day when visiting the Richardson Bay Audubon Center, you can find evidence of a crucial underwater ecosystem in the tangles of eelgrass along the high tide line. Comb through these errant blades and you’ll find different species of nudibranchs clinging on, and sometimes in late winter, the clear eggs of Pacific Herring lining the grasses. Salmon and sturgeon use the rich feeding grounds on their long migratory journeys. In fact, most creatures you can spot from the bay– the leopard sharks, harbor seals, and great flocks of waterfowl which can be seen during winter– all depend upon this mighty plant during some part of their life cycle. 
 


At the Richardson Bay Audubon Center and Sanctuary, we are devoted to eelgrass, which each winter transforms our bay into a sanctuary for thousands of wintering sea ducks. The ducks come to Richardson Bay because within it lies an eelgrass meadow, the most important breeding ground for Pacific Herring. The ducks time their migration with the herring spawning and by the time they get here, the eelgrass beds are lined with Pacific Herring eggs, the perfect meal for birds who have travelled thousands of miles and need to rest and refuel before flying back north. Eelgrass meadows are the base of a rich ecosystem, and they also provide a range of ecosystem services which benefit the communities around the bay. This seagrass stabilizes its environment by sequestering carbon and anchoring sediment to prevent erosion. It is also an extremely productive oxygen supplier, pumping oxygen directly into the water when it photosynthesizes, which improves water clarity and fish habitat. The gentle leaves of eelgrass can stifle powerful wave energy, which reduces flooding in large storm events. 


When water is diverted from our rivers, the composition of the whole estuary changes, and all the habitats within the estuary including beaches, mudflats, and eelgrass meadows are affected. The water becomes saltier, which causes stress and damage to the plants which populate it. Eelgrass can tolerate a specific range of salinity, and depending how far they are from the delta, changes in freshwater flow can push them outside of their ideal range. When water inflows change, the temperature of the water is also affected, which can affect algal growth and lead to Eelgrass Wasting Disease, a condition which is not yet widespread in San Francisco Bay but is in neighboring states. Eelgrass is found in shallow waters along nearly every continent, yet despite their ability to survive in nearshore environments across the world, they are more delicate plants than you might expect. They require some of the highest light levels of photosynthesizing species, and therefore are highly sensitive to sediment movement which clouds the water. Low turbidity and high light availability are requirements for eelgrass success across their entire range. This is part of the reason eelgrass ecosystems are crucial for understanding the health of the entire estuary, and why protecting these ecosystems is crucial. The health of eelgrass ecosystems bolster the health of native fisheries and bird populations, and create a stronger, more resilient Bay Delta. 


Looking Ahead 

The Bay Delta needs to sustain not only its residents and agrobusinesses, but also the nearly half of California's migrating waterfowl and shorebirds and two-thirds of the state's spawning salmon which pass through the Bay Delta. Balancing this delicate resource means focusing on protecting and conserving these vital habitats within the bay delta. Supporting these habitats in turn supports human systems. The delta, the estuary, and our freshwater systems are delicate, and solutions to these problems will require creativity and the ability to adapt to change. Protecting the estuary and its inhabitants can take many forms, and awareness of how different issues connect is one of the first steps. At Richardson Bay, we focus on protecting and advocating for eelgrass, and other important habitats that support birds along their migrations. When we invest in our natural resources, the ecosystems pay us back- not just through economic value, but by enriching our lives.

 

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