The most important piece of California’s water puzzle is the Sacramento-San Joaquin Delta, the 1,100-square-mile estuary where the state’s two most important rivers meet.

The Sacramento and San Joaquin rivers drain a watershed of mountains and hills that stretches about 400 miles from Mount Shasta, near the Oregon border, to the Sierra southeast of Fresno. After meandering through the dozens of channels and sloughs of the Delta, their combined waters flow into San Francisco Bay and thence to the Pacific Ocean – minus whatever has been diverted into cities and farms along the way.

And that’s the rub.

For decades, in political and legal forums, there’s been a great debate over how much water can be taken from the two rivers, their many tributaries and the Delta itself without destroying its natural function as habitat for fish and other wildlife.

Environmental groups and state water quality authorities, occasionally backed up by federal court decrees, contend that too much is being diverted, particularly by farmers. But the latter say that the water is needed to maintain California’s largest-in-the-nation agricultural industry.

For years, the state Water Resources Control Board has been on the verge of mandating sharp cuts in the diversions by raising Delta water quality standards. However, it has delayed what could be a high-stakes showdown over water rights, many of which stretch back more than a century, in hopes that satisfactory “voluntary agreements” could be reached.

Last week, a new chapter in the saga opened when environmental justice groups and Indian tribes filed a civil rights complaint with the federal Environmental Protection Agency against the board. It alleges that failure to issue those water quality standards gives preference to agricultural interests and violates the federal Clean Water Act.

Last spring, the same coalition submitted a 169-page petition to the water board, demanding that it issue new Delta water standards, but the board denied it, saying that updating was already underway.

The semi-permanent drought that’s plagued California adds urgency to the debate over the Delta because it reduces the overall supply of water to be divvied up among the various demands. Farmers and cities have experienced sharp cutbacks in deliveries from the federal and state canals that pump water from the Delta’s southern edge. Farmers also face new restrictions on how much they can draw from depleted underground aquifers to offset reductions in surface water.

The Public Policy Institute of California has estimated that the looming restriction on tapping underground water supplies alone will require at least 500,000 acres of farmland to be taken out of production. Permanent reductions in surface water that would result from higher water quality standards in the Delta would cause more farmland to be fallowed.

As the water quality clash plays itself out, another conflict over the Delta’s future looms –whether to bore a tunnel that would transport some Sacramento River water to the head of the California Aqueduct near Tracy, bypassing the Delta altogether. In one form or another, what’s now called the “Delta conveyance” has kicked around for six decades, first as a “peripheral canal,” later as twin tunnels and, since Gavin Newsom became governor, a single tunnel.

Advocates say such a bypass would solve some Delta water flow problems while providing more reliability in supplying water to Southern California, a central point of the environmental impact report issued by the Department of Water Resources a few months ago. However, critics contend that it would undercut efforts to increase flows through the Delta by reducing upstream diversions.

As the drought continues, how – or when – these intertwined Delta issues will be resolved remains the biggest mystery of California’s water supply conundrum.

Dan Walters is a CalMatters columnist.

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