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The Extremely Endangered San Joaquin River

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Last week, a prominent environmental group released its annual report identifying the top ten “endangered” streams and rivers nationwide—waterways that are at a crossroads politically, where key upcoming decisions will have major impacts for better or worse. California’s San Joaquin River, the second longest river in the state, is #1 on the list due to the historical and ongoing impacts of state water infrastructure, and major proposals to expand this infrastructure in the future. Flowing 330 miles, the River begins in the Sierra Nevada mountains and meanders through the San Joaquin Valley toward the Sacramento-San Joaquin Delta, which is part of the largest estuary on the west coast. Tributaries to the San Joaquin include the Stanislaus, Tuolumne, Merced, Calaveras, and Mokelumne Rivers. The 10,000 square mile San Joaquin Valley receives little rainfall on average, but historical river flows have been maintained by seasonal snow melt from the Sierras. This area is the most agriculturally productive region in the country; the San Joaquin Valley supports upwards of $25 billion in food crops annually. The San Joaquin River provides important transportation corridors for agricultural products and since the early 1900s, the river has been routinely dredged to allow large cargo ships to navigate. 


It is well documented that major changes to the Delta and the San Joaquin River have resulted from human activities, especially water diversions and other infrastructure that captures and transports water away from the Delta to drier parts of the state. Some studies estimate less than five percent of the native biodiversity of the Delta remains, with the tidal marsh habitats being most degraded. Chinook salmon and other native fish struggle to maintain healthy population levels as aquatic habitat areas along the San Joaquin (and many other waterways in and near the Delta) have been degraded and blocked by in-stream water diversions and monumental structures like dams.

 Water diversions and stream barriers reduce flows and physically alter the surrounding habitat areas. According to a report by the Public Policy Institute of California, many of these alterations and changes will be permanent: [t]he characteristics of the earlier Delta that are likely gone forever include (1) physical habitat appropriate for species that tend to rely on shallow water and structure for refuge and feeding; (2) food aggregation that long, complex sloughs and channels provide through increased production and retention, and (3) cooling functions that adjacent wetlands provide for small water bodies, such as sloughs, which provide refuge for fishes during summer heat spells.


Today, biologists carefully monitor and manage fisheries in the San Joaquin. Because of excessive water diversions which cause the San Joaquin River to literally run dry in several places, including at the site of the Friant Dam, biologists must intervene directly by capturing and transporting anadromous fish down river.

Endangered species lawsuits have successfully argued that some of this dewatering and ongoing ecological harm must be mitigated by reducing or timing water diversions to maintain adequate flow levels in the future. The Delta Smelt, a small fish native to the confluence of the San Francisco Bay and the Sacramento-San Joaquin Delta, have long been the bane of agricultural and conservative political interests in the San Joaquin Valley. After decades of litigation, a recent appeals court decision determined that the U.S. Bureau of Reclamation and the State of California, which manage the Central Valley Project (CVP) and State Water Project (SWP) respectively, must consider flow levels and other impacts to endangered species habitat when determining the price and delivery schedules for CVP and SWP water.


Subsurface water resources are also affected by development and flow diversions on the San Joaquin River. It has been nearly 150 years since water was first diverted from this area, and over 120 years since irrigation colonies were established in the San Joaquin Valley. During much of this time, more water was pumped out of local aquifers than was recharged, with deficits as high as 800,000 acre-feet per year during the mid-1900s. Reduced flows also impact salinity by allowing saltwater intrusions in surface streams as well as aquifers. Subsidence is also on ongoing issue due to groundwater overdraft and several other environmental factors.

The future of the San Joaquin River is closely tied to public policy actions that are currently being debated. Governor Brown’s controversial Bay Delta Plan would create additional “peripheral” tunnels to transport more water away from the Delta to urban and agricultural areas further south, and would also attempt to restore habitat areas that have been (and will be) impacted by state water infrastructure. Opponents of this plan emphasize the ecosystem losses that will occur if heavy duty infrastructure continues to expand, the lack of capacity for more water diversions from fragile riparian systems, and the uncertainty regarding how proposed ecosystem restoration will go. Proponents of the plan emphasize the state’s growing need for water, particularly in light of California’s three-year drought, and the lack of good options elsewhere.


Decisions regarding the Bay Delta Plan and the San Joaquin River will also have community impacts, particularly in rural areas. Communities in the San Joaquin Valley will deal with a decade or more of construction if new tunnels are approved. Farmworkers already bear the brunt of drought-related income loss, and this group is likely to remain highly vulnerable to the effects of water shortages. Rural communities are experiencing water shortages especially in areas where communities rely on water from a single water source like the SWP. As demand for water grows, communities and groups with the least economic power will continue to suffer most.

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Annie Beaman is an independent consultant working on water issues and sustainable agriculture in California. In addition to researching, writing, strategizing, and campaigning about issues that impact vulnerable ecosystems and communities, she is an avid gardener and baker. Annie is a stewardship-obsessed member of a multi-generational farming family, and a longtime advocate for environmental protection and social justice. Follow her on Twitter @anniebeaman.


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