“Sediment has been identified as a significant contributor to the aggradation of the San Joaquin River and reduces its capacity to carry flood waters.” — Excerpt from the December 1992 report by the Department of Interior Fish & Game Wildlife Service prepared for the Army Corps of Engineers

California’s natural cycle — if you haven’t figured it out by now — consists of long periods of drought followed by periods of heavy rain and snow.
There is a reason why early explorers described the Great Central Valley as a marsh in the winter and spring and arid area in the summer and fall. What keeps that cycle in check most of the time are the levees in the Delta and along the rivers and dams in the Sierra.
As Manteca was reminded of 20 years ago, when a heavy snowpack is suddenly pelted with steady and relatively warm rain you get massive  runoff from snow melt.
Much of that snowmelt between the Southern and Central Sierra converge south of Manteca near the Airport Way bridge. It is funneled from its confluence with the Stanislaus River at Vernalis into a short stretch of the San Joaquin River before it diverges into two channels – the Old River and the New River — to meander through the Delta just after the Mossdale Crossing in Lathrop.
Logic would dictate that making sure the San Joaquin River from Vernalis to Mossdale can handle high volumes of water is a smart move especially given government reports have referenced a need to dredge the stretch.
 State and federal government agencies steadfast refuse to look at sediment build-up on the San Joaquin River between Vernalis and Mossdale as a major contributor to flooding even though it has already confirmed dredging will significantly reduce the chance of flooding in Manteca, Lathrop, and nearby areas.
The Soil Conservation Service in 1992 determined streambank erosion was not a major contributing factor to sedimentation build up on the San Joaquin River. Instead the primary source of sediment build-up was from furrowed farmland land from the West Stanislaus County area.
A study discovered that sediment run-off at the confluence of the Eastside Bypass and the San Joaquin River had created a “serious flood problem.” The design capacity had been decreased from 16,500 cubic feet per second (cfs) for water movement to less than 7,000 cfs. That study led to the Army Corps spending $2.3 million on dredging to restore 30 percent of the lost channel capacity and significantly reduce upstream flood potential.
There are now measures in place to reduce sediment run-off from Westside farms.
But the big question is how did the mess with sediment build-up on the Lower San Joaquin River that impacts Manteca and Lathrop get started? After all levees were in place for nearly a century with no measureable build-up as barges carrying wheat were able to go as far south as what was once San Joaquin City near Vernalis 10 miles to the southwest of Manteca without an issue. It is an area now that is laden with sand bars visible as river flows recede.
The answer may surprise you. The sediment build-up is courtesy of water system engineered in a vacuum by federal agencies such as the Bureau of Reclamation and Army Corps of Engineers. The Central Valley Project — specifically with the creation of Friant Dam — changed the San Joaquin River. Reduced flows in part led to more vegetation growth on the river below Friant reducing channel capacity.
Worse yet, water management practices encouraged by federal agencies after Friant Dam’s completion led to disastrous selenium build-up at the Kesterson Wildlife Refuge. Subsequent switches of water sources for the Westside involving various canals changed the quality of water in terms of how much sediment it carried that was being dumped into the San Joaquin River and monitored at Vernalis.
While extensive studies of sediment build-up in the Lower San Joaquin between the confluence of the San Joaquin and Stanislaus rivers and Mossdale Crossing where the Old River splinters from the main San Joaquin River channel have not been done, they were promised as part of the 2000 water bond. Before a study could be funded the legislature siphoned off funds during a state budget crisis to keep the Department of Water Resources bureaucracy running.
Long-time river observers — including the late and well-respected “citizen” water expert Alex Hildrebrand — believe the bottom of the San Joaquin River south of Manteca and Lathrop has risen by as much as seven feet since 1959.
That observation seems to be backed up by sand bars that have become more frequent during the past 25 years as well as the simple fact upstream sediment such as at the Eastside Bypass eventually makes it way downstream.
The return of irrigation water from Westside farmers that for years was brownish meaning it was laden with soil flowed into the San Joaquin River at Vernalis. There are measures now in place that are virtually eliminating that issue.
A channel dredged back to 1959 parameters would likely drastically alter modeling for state-mandated 200-year flood protection. It could make the controversial cross or dry levee extension in rural south Manteca superfluous. Better yet, it would reduce the potential for the bigger worries which are seemingly frequent 100-year flood events.
The Army Corps — as  well as other state and federal bureaucracies — won’t touch river dredging with a 10-foot pole.
It’s either because of complicity with environmental perfectionist groups or fear of them in today’s politically correct world that has given dredging the treatment once reserved for leprosy victims.
Government agencies have made it clear dredging is a solution that won’t even make it onto the table.
How ironic is that given the Army Corps of Engineers in study after study until they started cowering before the PC Movement took control consistently listed the elimination of sediment build up along with vegetation control, levee structural reliability, and operational decisions regarding water releases as the four essential components needed to be addressed simultaneously to significantly reduce flooding in the 14,000-square-mile San Joaquin River Basin.