The USGS study found that land sinking had been measured at nearly one-foot per year in one area, and that it is reducing the flow capacity of the Delta-Mendota Canal and the California Aqueduct, two key sources of water.
"We were surprised at the amount of land being affected," said Michelle Sneed, a USGS hydrologist and the report's lead author. "We were also surprised by the rapid rate of (sinking)."
Because canals were built with a small slope to propel the water, sinking land can change that slope in random areas and affect flows, Sneed said.
The U.S. Bureau of Reclamation, which operates the canals, will use the USGS data to mitigate damage and factor into current and future construction projects.
"Nothing to date, to my knowledge, has affected our ability to deliver water to our customers," said Richard Woodley, the bureau's assistant regional director. "Our main point is to get ahead of that."
The issue of sinking land in the San Joaquin Valley is not new, but had slowed in recent decades after the construction of the California Aqueduct and Delta-Mendota Canal.
Those canals helped meet water demand from farms and growing Southern California with waters flowing on the land surface, which reduced demand on aquifers.
But the sinking problem in the two years studied 2008-2010 was exacerbated by drought, the report found.
In those dry years, there was less rain, but also limits placed by water regulators on surface water use. This caused farmers and others to increase the amount of water pumped from underground; there are no restrictions on groundwater pumping in California.
Canals aren't the only area at risk, USGS said.
Railways, roads and pipelines things that extend over a long distance are also under threat from an increase in the rate of ground sinking, Sneed said.
For California's bullet train project, which would speed through the Central Valley, the sinking ground is being taken into account for the system's design, Frank Vacca, the chief program manager for the California High Speed Rail Authority.
He said the rail system will be made of a flexible material that can give into movement.
"This is just one more box to check on our list of engineering considerations," Vacca said.
Woodley said the issue has already affected construction projects on the massive San Joaquin River restoration, already projected to cost $1 billion.