Water in the canal comes from Millerton Lake, behind Friant Dam and is supposed to move downhill all the way into Kern County, but the ground underneath the canal has started sinking so the water is no longer moving as it should.
"It's been so pervasive it's caused the canal to drop almost six feet in the past couple of years," Doug Deflitch said.
Doug Deflitch is the Chief Operation Officer of the Friant Water Authority in charge of operating canal. He says there's a big stretch that is sunk or subsided, basically turning the section of the canal into a deep pool, stopping the flow.
"So with the canal being so long 152 miles you have that maybe 20 miles or so of subsidence that have occurred and so the locations below there diminished in capacity," Deflitch says.
Diminished by up to 60 percent, the water in the canal is supplied by the Federal Bureau of Reclamation and Area Director Michael Jackson says the sinking land is affecting all of the valley's primary irrigation canals.
Jackson said, "We are seeing it on the Friant Kern, we are seeing it on the Delta Mendota Canal, as well as the California Aqueduct."
The sinking is the result of farmers pumping underground water during the drought.
NASA measurements show the entire Central Valley sank so much as the water was pumped out it pushed the Sierra and coastal mountain ranges up half a foot in just a few years. Something that would normally take millions of years.
Growers say they had no choice since there was not enough water coming through the canals during the drought. Now, as a result of the damage caused by pumping so much underground water, there will be less water in the canals, and a huge repair bill to raise the canals and bridges that cross over them.
"It's in the hundreds of millions of dollars," Deflitch said.
Irrigation districts and the federal government will likely share the costs of the repairs to water structures, but a UC Davis study estimates the total price tag for the damage by the valleys sinking land to roads, utilities, and properties at two billion dollars.