California’s Sacramento-San Joaquin Delta – a short history of big changes

Land subsidence in California’s Sacramento-San Joaquin Delta

by Jay Lund

Deltas globally adjust with changes and fluctuations in external conditions, internal dynamics, and human management.  This is a short history of big changes to California’s Sacramento-San Joaquin Delta (Delta) in the past and present, and its anticipated future.  This history is important for understanding how many of the Delta’s problems have developed, changed, and continue to change.

Sea level rise. California’s Delta is a product of sea level rise.  At the end of the last Ice Age, about 11,000 years ago, the sea was about 300 feet below today’s levels and the delta from the Sacramento and San Joaquin rivers formed in the Pacific Ocean, outside the Golden Gate.  As sea level rose, San Francisco Bay flooded, and about 6000 years ago, the rising sea level began to drown the confluence of the Sacramento and San Joaquin rivers, forming an inland delta at the Delta’s present location.  Sea level rise during this latter period was slow enough that the resulting immense tidal freshwater marsh arose with the sea level, forming the Delta’s deep peat soils of partially decomposed marsh plants.  These peat soils typically are deepest in areas longest affected by sea level rise.  Before 6000 years ago, today’s Delta was not a delta at all, but a river corridor subject to probably extensive seasonal flooding. (Atwater and Belknap 1980)

Poldering.  From the 1850s until the 1930s, most of the Delta’s 750,000 acres of wetlands were diked and drained to produce today’s agricultural Delta islands and tracts, which are predominantly agricultural with a few towns.  The Delta was California’s first large irrigated area, with year-round access to fresh water, near sea-level elevations that supported both field flooding and drainage with the tides, and location on steamship routes to markets.  However, the drainage of peat soils quickly accelerated their chemical decomposition, lowering the elevation of many island interiors by up to several inches per year.  After several decades, lowering lowland elevations required pumping for drainage and increasing costs for maintaining Delta dikes.  This dominant agricultural land use and increasing drainage and flood risk costs from land subsidence continues today, with occasional abandonment of islands to become flooded tracts (such as Big Break, Franks Tract, Mildred Island, and Liberty Island).  (Thompson 1957; Weir 1950)

Upstream diversions.  In the late 1800s, irrigation expanded using water upstream of the Delta, diverting from the Sacramento and San Joaquin rivers, and their tributaries.  Without major reservoirs, these upstream diversions occurred predominantly in the summer, and largely depleted summer inflows to the Delta in dry years during the early 1900s.  In the 1924 drought, the Carquinez Strait sugar plant was sending barges west to Marin, instead if east to the Delta, for freshwater.  By the 1930s drought, summer seawater intrusion extended inland to near Stockton.   Even today, most water taken from the Delta is diverted upstream. (Jackson and Paterson 1977)

In-Delta diversions.  By the 1930s, plans were being made to build reservoirs above the Central Valley to store water from winter for summer water supply and build pumps and canals from the Delta to thirst parts of the Bay Area, San Joaquin Valley, and southern California.  Preventing seawater intrusion by building a dam west of the Delta was considered, but rejected due to its high costs compared to the water cost of a “hydraulic barrier” of required Delta outflows.  Major in-Delta diversions began in 1949 by the USBR Central Valley project, growing faster with the State Water Project, to the present time.  These major in-Delta diversions, especially those from the southern Delta, caused major changes in the flow directions and magnitudes in Delta channels, and tied the Delta even more to the state’s economy as a whole. (DWR 1931)

Invasive species.  From the time of the Gold Rush, non-native species have been introduced to the Delta by ships hulls and ballast water, fishermen, fish agencies, and household aquarium owners.  Today’s Delta ecosystem is dominated by non-native species.  The Delta seems destined to be dominated by non-native species in highly altered habitat. However, efforts can be made to manipulate conditions to be more conducive for native species overall, recognizing that most non-natives will be impossible to eradicate. (Moyle et al. 2012)

Climate change.  Climate change will continue to shape the Delta, likely more rapidly than in the past century, especially from more rapid sea level rise and higher temperatures.  The maintenance of some subsided Delta islands will become less sustainable, with higher sea levels, continued land subsidence, less summer and more winter inflows (due to loss of snowpack), and more frequent flood flows and high water.  Temperature increases and more frequent droughts seem likely to further squeeze some native species and facilitate expansions of non-native species.  (Brown et al. 2013; DISB 2020)

Other human-induced changes.  Additional human-caused changes in the Delta should be expected from increased economic demands for Delta water exports from ending groundwater overdraft and more valuable agriculture, changes in conveyance and storage infrastructure, increased management for native species, and changes in environmental regulations and regulatory approaches (such as voluntary agreements).

What this means for Delta science and management.  Changes build upon changes.  Many old changes will continue, like sea level which has always defined the Delta, and there are more, mostly faster, and different changes to come.  The Delta’s ecosystems, water supplies, and communities will be challenged by these changes.  Managers, policymakers, and Delta communities will have to deal with all of these changes altogether – not one by one.  To be prepared, our scientific efforts must face these challenges in advance.

Historically, managing the Delta was about making planned changes, building and operating levees, pumps, canals, and land uses to provide services.  The future will include making planned changes, but management will increasingly be responding to changes driven from outside the Delta and the internal dynamics of Delta landscapes and ecosystems. 

Delta smelt - Wikipedia
Delta smelt

Further readings

Atwater, Brian F. (1982), Geologic maps of the Sacramento-San Joaquin Delta, California, Miscellaneous Field Studies Map 1401, USGS,

Atwater, B. F. and Belknap, D. F., 1980, “Tidal-wetland deposits of the Sacramento – San Joaquin Delta, California,” in Field, M. E., Bouma, A. H., Colburn, I.P.-;-Douglas, R. G., and Ingle, J. C., eds., Quaternary Depositional Environments of the Pacific Coast: Society of Economic Paleontologists and Mineralogists, Pacific Coast Paleogeography Symposium 4, p. 89-103.

Brown, Larry R., et al. “Implications for Future Survival of Delta Smelt from Four Climate Change Scenarios for the Sacramento–San Joaquin Delta, California.” Estuaries and Coasts, vol. 36, no. 4, 2013, pp. 754–774., doi:10.1007/s12237-013-9585-4.

Delta Independent Science Board, “Preparing for a Fast-forward Future in the Sacramento-San Joaquin Delta,” August 10, 2020 (Draft paper)

Division of Water Resources (1931), Report to the Legislature on State Water Plan 1930, Bulletin 25, State of California Department of Public Works, Sacramento, CA.

Jackson, W. T., and A. M. Paterson, The Sacramento–San Joaquin Delta and the Evolution and Implementation of Water Policy:  An Historical Perspective, California Water Resources Center, Contribution No. 163, University of California, Davis, June, 1977.

Lund, J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle, Envisioning Futures for the Sacramento-San Joaquin Delta, Public Policy Institute of California, San Francisco, CA, 300 pp., February 2007.

Lund, J., E. Hanak, W. Fleenor, W. Bennett, R. Howitt, J. Mount, and P. Moyle, Comparing Futures for the Sacramento-San Joaquin Delta, University of California Press, Berkeley, CA, February 2010.

Malamud-Roam, Frances, Michael Dettinger, B. Lynn Ingram, Malcolm K. Hughes, and Joan L. Florsheim. (2007), “Holocene Climates and Connections between the San Francisco Bay Estuary and its Watershed,” San Francisco Estuary and Watershed Science. Vol. 5, Issue 1 (February). Article 3. 3

Moyle, P., W. Bennett, J. Durand, W. Fleenor, B. Gray, E. Hanak, J. Lund, and J. Mount (2012), Where the Wild Things Aren’t: Making the Delta a Better Place for Native Species, Public Policy Institute of California, San Francisco, CA, 55 pp., June.

Moyle, Peter B., et al. (2013) “Climate Change Vulnerability of Native and Alien Freshwater Fishes of California: A Systematic Assessment Approach.” PLoS ONE, vol. 8, no. 5, 2013, doi:10.1371/journal.pone.0063883.

National Research Council. A Review of the Use of Science and Adaptive Management in California’s Draft Bay Delta Conservation Plan. National Academies Press, 2011.

Thompson, John, 1957, Settlement geography of the Sacramento San Joaquin Delta: Stanford University, Ph.D. thesis, Stanford, California, 551 p.

Weir, W., 1950, “Subsidence of peat lands of the Sacramento – San Joaquin Delta, California,” Hilgardia, v. 20, p. 37-56.

Whipple, A.; Grossinger, R. M.; Rankin, D.; Stanford, B.; Askevold, R. A. 2012. Sacramento-San Joaquin Delta Historical Ecology Investigation: Exploring Pattern and Process. SFEI Contribution No. 672. SFEI: Richmond.

Jay Lund is a Professor of Civil and Environmental Engineering and Co-Director of the Center for Watershed Sciences at the University of California – Davis

About jaylund

Professor of Civil and Environmental Engineering Director, Center for Watershed Sciences University of California - Davis
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1 Response to California’s Sacramento-San Joaquin Delta – a short history of big changes

  1. Joseph Rizzi says:

    Dredging — Importing Salt Water to ports of Sacramento and Stockton while also exporting our FRESH water out of the Delta faster. YOU MISSED this one!! It is easily overlooked but it is the most important all for the shipping goods. Add a lock and louvers at 1/2 of Benicia bridge to restrict Salt Water intrusion and leave north 1/2 open for environment. That will fix our problems.

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