The San Joaquin Valley is a vast agricultural powerhouse – and ground zero for many of California’s most pressing water management challenges. Seven of the state’s top 10 agricultural counties are in the San Joaquin Valley, and the valley’s orchards, farms and dairies account for well over half of the state’s $67 billion gross crop values. But the valley also is highly dependent on water imported from Northern California or pumped from deep underground – pumping that has damaged roads, bridges and essential water infrastructure. Naturally occurring elements or human-engineered chemicals have tainted some of the valley’s groundwater and many of the valley’s historic wetlands have been drained and farmed. The valley is now in the midst of a decades-long effort to halt depletion of its groundwater through better management of pumping and more expansive aquifer recharge.

BACKGROUND

Located in the middle of California, the long and flat San Joaquin Valley is bracketed on the west by the Coast Ranges and on the east by the towering Sierra Nevada. The valley’s hot, dry summers are followed by cool, foggy winters that make it one of the most productive agricultural regions in the world. The region includes large cities such as Fresno and Bakersfield, national parks such as Yosemite and Sequoia & Kings Canyon, millions of people and millions of acres of fertile farmland.

Almost since the state’s founding in 1850s, the San Joaquin Valley has drawn people eager to exploit its vast tracts of rich soil and snow-fed streams from the Sierras. Irrigation began in the San Joaquin Valley in the 1870s and some of the state’s titanic water rights clashes were fought there, shaping laws that today govern who has first rights to water and how it must be used. But with the expansion of irrigated agriculture and improvements in pumping technology, the valley’s water table began dropping, bringing an end to the artesian wells that once flowed.  

By the early 1930s, with California mired in another extended drought and concerns growing about the valley’s declining groundwater table, the state’s voters approved a bond measure to fund a state-operated Central Valley Project (CVP). But in the harrowing depths of the Great Depression, California was unable to find a buyer for its bonds. The federal government, looking for projects that would put people back to work, agreed to take it over.

Thus began construction over the next four decades of an extensive network of canals, dams and other features designed to store and move water in the Sacramento and San Joaquin valleys. Among the CVP’s key features are Shasta Dam, which impounds the Sacramento River near Redding for later use in both the Sacramento and San Joaquin valleys, and Friant Dam, which impounds the San Joaquin River near Fresno. The CVP and the State Water Project (SWP), constructed mainly in the 1960s, have fueled an expansive and diverse agricultural economy.

Meanwhile, other rim dams in the foothills of the Sierra Nevada have impounded water for hydroelectric power generation, flood control and irrigation purposes and altered the historic landscape.

Tulare Lake, a seasonal dry lake and tule marsh complex that once dominated the San Joaquin Valley landscape, would be filled each winter and spring by rainfall and snowmelt from southernmost Sierra Nevada rivers such as the Kings River. By the end of the hot San Joaquin Valley summer, the giant lake – once the largest freshwater body west of the Mississippi River – could disappear primarily due to evaporation.

The development of diversions and dams along the southern Sierra foothills, particularly Pine Flat Dam, an Army Corps of Engineers facility on the Kings River, held back the flows in most years from refilling the lake, allowing farming to replace the seasonal wetlands.

Today, across the expansive San Joaquin Valley, growers raise a multitude of fruits, vegetables and field crops, including grapes, nuts, tomatoes, citrus and cotton.

CHALLENGES AND CONTROVERSIES

On the west side of the San Joaquin Valley, drainage and disposal of salty water from irrigated agricultural fields has been a longstanding challenge. Soil on the valley’s west side is naturally rich in salt and trace minerals such as selenium – a geologic legacy from when the area was a long-ago part of the Pacific Ocean. Water imported from the Sacramento-San Joaquin Delta by federal and state water projects brings tons of salt to the area (the equivalent of about 40 railroad cars daily according to estimates). The dense, clay soil prevents the salty water from permeating deeply and instead it becomes part of the shallow groundwater table. The salty water collects and rises to the surface, drowning plants. In areas without such an impermeable layer, the leached water percolates into an unconfined groundwater aquifer.

The Bureau of Reclamation started but never completed the San Luis Drain, intended as a CVP project to carry saline drainage to the Sacramento-San Joaquin Delta. Years of litigation by Westlands Water District and some of its farmers led to settlements with the Bureau of Reclamation and the retirement of about 100,000 acres of farmland from irrigated agriculture. Westlands now is responsible for managing agricultural drainage within its district.

Construction of Friant Dam in the early 1940s diverted most of the San Joaquin River’s flows to farms and cities on the east side of the valley. But the dam also dried up portions of the San Joaquin River, causing the demise of what was once the nation’s largest spring run of chinook salmon. After nearly two decades of litigation over the loss of the fishery, a settlement reached in 2006 laid the foundation for the San Joaquin River Restoration, a project to bring back a self-sustaining salmon fishery to the river while limiting adverse water supply impacts to farmers. In 2019, for the first time in more than 65 years, spring-run salmon released as juveniles returned from the ocean to spawn in the river.

Groundwater has been an important source of irrigation water for San Joaquin Valley farmers, particularly in drought years when surface water supplies are limited. But excessive pumping has significantly lowered the water table, causing the surface of the land to subside. That has caused damage to canals and aqueducts that lace the valley. The 152-mile Friant-Kern Canal, which delivers water to 1 million acres of farmland and more than 500,000 people from the Fresno area south to Bakersfield, lost 60 percent of its design capacity in a section in Tulare County due to subsidence. In 2021, the Friant Water Authority launched a $500 million project to repair a 33-mile stretch of the canal to restore capacity. Other water conveyance facilities have also been damaged.

California had largely left groundwater unregulated until 2014, when the Sustainable Groundwater Management Act was enacted. Groundwater Sustainability Agencies throughout the valley have developed plans to bring groundwater pumping into balance with recharge of the aquifer. The agencies have until 2040 or 2042, depending on their degree of overdraft, to bring their groundwater basins into balance.

LOOKING AHEAD

Achieving groundwater sustainability will be an ongoing challenge for the San Joaquin Valley and will likely require hundreds of thousands of acres to be taken out of irrigated agriculture or otherwise repurposed. Facilities to capture stormwater in wet years and move it to places where it can easily soak into the aquifer will need to be built and agencies will have to navigate the state’s water rights system to capture high-water flows for recharge without impinging on existing water rights.

Adding to the challenge is climate change, which is expected to bring more extreme wet and dry years and change precipitation patterns. More of the winter bounty is expected to fall as rain and less as slow-melting Sierra snow. That may add to the complications faced by farmers, water managers and communities living and working in the San Joaquin Valley.

 Updated June 2026