The Sacramento-San Joaquin Delta: pumps, smelt and sinking islands

The Sacramento-San Joaquin Delta is where the Sacramento and San Joaquin rivers meet before reaching San Francisco Bay.¹⁸ Pumps in its south end draw water for the State Water Project and the federal Central Valley Project, part of a water system that supplies more than 27 million Californians.^15,17 The same water is home to the delta smelt. The state's Fall Midwater Trawl, run every autumn since 1967 except 1974 and 1979, gave the smelt an index of 408 in its first year and 2 in 2017. The index has been zero in every year from 2018 through 2025.^1,2 The UC Davis Fish Conservation and Culture Laboratory, which holds a refuge population, now produces about 125,000 smelt a year, and hatchery fish have been released into the wild since 2021: 163,349 of them at Belden's Landing and Rio Vista in November and December 2025.^3,4,5,6 By late May 2026 monitoring surveys and the fish salvage at the federal pumps had recorded 44 adult and 30 juvenile delta smelt.⁴ The longfin smelt of the Bay-Delta has been federally endangered since August 2024.⁷ Around all of this run 1,100 miles of earthen levees, and only about 30% of the islands and tracts have levees that fully meet state or federal design standards.¹⁷ The drained peat on the islands keeps breaking down. On the developed islands of the central and western Delta the land has sunk at long-term average rates of 1 to 3 inches a year, and large areas of many islands now lie more than 15 feet below sea level.¹⁸

Three decisions fall close together. In December 2025 the Bureau of Reclamation adopted a revised federal operating plan, called Action 5, in answer to a January 2025 executive order to increase deliveries.⁸ It dropped the Delta Summer and Fall Habitat Action.⁸ Reclamation says it may add 130,000 to 180,000 acre-feet a year to federal deliveries, and 120,000 to 220,000 to the state's, depending on how wet the year is and on the state adopting Action 5 too.⁸ On 28 and 29 October 2026 the State Water Resources Control Board meets to consider new flow rules for the Sacramento River, its tributaries and the Delta.^9,10 Water-rights holders in the Healthy Rivers and Landscapes agreements would follow a voluntary path, and holders of other water rights a regulatory one.^9,10 The third is the state's Delta Conveyance Project: two intakes on the Sacramento River near Hood, and a tunnel about 45 miles long to a new pumping plant at Bethany Reservoir.¹² In April 2026 the Delta Stewardship Council voted six to one on ten appeals against it.^12,13,14 It rejected most of their claims but sent the project back to the Department of Water Resources over the habitat it could give the invasive golden mussel and its conflict with the Sacramento Area Sewer District's Harvest Water recycling programme.¹² The Department of Water Resources filed a revised certification on 24 July 2026.¹⁵

Who needs an answer

• The State Water Board, deciding this month how much water must stay in the rivers and the Delta, and through which path.⁹
• The operators of the state and federal pumps, who each week weigh exports against fish triggers set on turbidity and temperature.⁴
• The wildlife agencies and the hatchery, deciding how many cultured smelt to release and where, and whether releases can stand in for habitat.^3,5
• The Department of Water Resources and its water contractors, deciding whether to build the tunnel. Against it, the appellants: Delta counties, Tribes and the city of Stockton.¹²
• Levee districts and the state agencies that fund them, choosing which islands to protect first.¹⁷

The domains it chains

Rain and snowmelt upstream set how much water reaches the Delta. The leveed islands themselves help keep salt water away from the pumps.¹⁸ Pumping is capped by how far negative it drives the flow index in the Old and Middle rivers, and the rules tighten for smelt when the water runs turbid.⁴ Hatchery fish now join a wild population the autumn trawl no longer registers.^1,4 The exports supply water across the state. On the islands, peat soils lose carbon as they sink, and the levees hold back water higher than the farmland and homes behind them.¹⁸ The new plan would also formally protect Tribal uses of water.⁹

What a twin should let people try

• Trade-off: under the new flow rules and under Action 5, how much water is exported in wet years and dry ones, and what happens to smelt habitat and salinity?
• Supplementation: if the hatchery reaches its plan of 500,000 fish a year by 2030,⁵ how many need to survive and spawn for the wild population to hold, and does it matter where and when they go in?
• The tunnel: with intakes in the north Delta, how do flows in the interior channels and salinity at the south Delta pumps change, and could the intakes and tunnel give invasive golden mussels new habitat?¹²
• A levee break: if a deeply sunken island floods in a storm, how far does salt water move, how long are the pumps shut, and which repairs would have prevented the most harm?

Where to start

The state publishes the Fall Midwater Trawl indices back to 1967.^1,2 The US Fish and Wildlife Service publishes Enhanced Delta Smelt Monitoring reports with weekly abundance indices and a summary of releases.³ The Bureau of Reclamation's Bay-Delta Office posts a weekly fish and water operations outlook with the status of each trigger.⁴ River flows come from USGS water data. The Delta Stewardship Council plans a high-quality elevation map of the whole Bay-Delta, and a Delta-wide 2D flood model built on it for any agency to use.¹⁷ An estuary model such as Delft3D can carry flow and salinity; a food-web model such as Ecopath with Ecosim can take the fish. The use case on flooding and rivers lists more.