El Nino Planning Must Include Dredging
On September 21, Governor Gavin Newsom declared a state of emergency due to the “strong and likely historic El Nino event in the Pacific Ocean.” The timing of the announcement is in response to the latest predictions from the National Oceanic and Atmospheric Administration, estimating a 90 percent chance of a “very strong event during the Northern Hemisphere fall and winter of 2026-27.”
In the Executive Order that accompanied Newsom’s emergency proclamation, he directs state agencies to “prioritize permitting, consultation, and technical assistance to support local efforts,” and among the efforts noted are “sediment management” and “channel-capacity improvements.” He does not, however, specify the area where sediment buildup poses the most acute danger to the entire state, which is the Sacramento-San Joaquin Delta.
The main stem of the San Joaquin River, as well as most channels in the southern delta, are dangerously clogged with sediment. If the predicted super El Nino brings extreme rains, flood waters will overwhelm the levees. The disastrous floods that hit when the San Joaquin overflowed in 1997 mostly inundated open space, but today much of that area has new homes.
The threat isn’t limited to farms and cities in and around the delta, however. Dredging the delta, starting with the southern channels, could prevent a statewide catastrophe. Only four channels in the south delta supply water to the Clifton Court Forebay, which is where water is collected for the pumps to supply the California Aqueduct (state) and the Delta Mendota Canal (federal). All of these channels are dangerously clogged with silt.
If a series of El Nino storms cause multiple levee breaches, the flooding will not only destroy homes and businesses, but also will cause land-based urban and farm chemicals to mix with the floodwater. The below sea level islands with broken levees will also absorb sea water. The combination of high salinity and contaminants could shut down pumping into the aqueducts for months.
The Great Valley Farm Water Partnership, a coalition that has united farmers throughout the San Joaquin Valley, has patiently advocated dredging for several years. It was once routine. For over a century, ever since the levees were built, the government and private landowners conducted ongoing dredging operations. Up until the 1970s, deep delta channels were maintained and, notably, the fish thrived. But since then, with the exception of shipping channels, dredging has ceased for the most part. This is due to extremely high costs for environmental permits, combined with dramatic reductions in the time permitted for dredging operations.
The estimated cost to dredge delta channels today is around $10 million per mile. Dredging the most severely affected 75 miles of channels in the south delta could be done for under $1 billion. In a relaxed permitting environment, which is a necessity if the work is to be done soon, costs might even be lower. This is a small price to pay to restore enough flow capacity to make a catastrophic flood event far less likely.
Another way to reduce the risk of major flooding this winter would be to divert more water from the delta tributaries for groundwater recharge. Newsom’s proclamation only obliquely addresses groundwater recharge, even though diverting floodwaters to percolate relieves pressure on downstream levees. Why doesn’t Newsom’s latest executive order suspend the regulations in the State Fish and Game Code, Public Resources Code, and Water Code, that inhibit the ability for farmers and irrigation districts to divert floodwater onto percolation basins on their own land? He did this in 2023, and he needs to do it again. It should take effect immediately and remain in force forever.
The failure of the state to resume dredging in the delta is inexplicable when considering the many additional benefits. Restoring channel capacity would mean that more water can be kept in upstream reservoirs. As it is, because the flow capacity in the delta is reduced due to silt accumulation, reservoir managers have to release more of their stored water in anticipation of spring storms.
Dredging also will prevent delta irrigation channels from running dry. The supply channels are so shallow that portions of them now have no water during the summer months. This problem would be solved if channel depths were restored. Farm irrigation in the delta does not consume water, by the way, because nearly all of it percolates right back into the channels.
Environmental benefits are one of the most unrecognized results from dredging. Widespread mechanical dredging in the delta was ongoing from the 1880s through the 1970s. Salmon migrated up the deep, cool channels when there was dredging, and smelt hid from predators in the turbid (cloudy) water. Today, shallow, warm channels favor invasive fish and plant species.
Deeper channels also have more flow capacity, which means normal spring flows will have a slower velocity. Currently, salmon fingerlings are often washed out to sea before they’re big enough to evade predators. In slower moving channels they can stay upstream longer, improving their survival.
Dredging also removes non-native aquatic plants. As noted, these plants thrive in warm and shallow water. They displace native plants and cause additional obstruction to channel flows. Dredging removes them in bulk. Restoring channel depths also improves circulation, water quality, dissolved oxygen, and reduces algae.
Finally, the so-called “spoils” of dredging: millions of cubic yards of removed silt. It is not only useful to help reinforce the adjacent levees, but can also be used for habitat restoration in downstream estuaries in the delta and San Francisco Bay. Engineered marsh habitat would not only benefit aquatic and avian wildlife, but it could absorb the nitrogen in the effluent from Bay Area wastewater treatment plants.
While Newsom has declared a state-of-emergency, he needs to do more. He needs to waive the permitting process that makes it hard to divert floodwater into percolation basins. And he needs to work with the Trump administration and the Army Corps of Engineers to get dredging equipment into the worst, most obstructed channels, and remove sediment.
In a more practical, less polarized age, all of this would have already been done.
Edward Ring is the director of water and energy policy for the California Policy Center, which he co-founded in 2013. Ring is the author of several books, including The Abundance Choice – Our Fight for More Water in California (2022), and The Analyst’s Cookbook: Making the Case for Abundance Using Numbers (2026).