When the San Joaquin River restoration begins Thursday, farmers and government officials will be watching for something pretty rare on the west side of the Valley — too much water.

They’re concerned that in some stretches of the river — where it hasn’t flowed for decades — water could seep into the ground, overfilling aquifers and drowning crops.

The danger of water flowing over the banks is small. The U.S. Bureau of Reclamation says it won’t introduce more water than the river channel can handle.

Because the government will improve the water channels as part of the restoration process, long-term flooding dangers actually may lessen as a result of the river project, officials said.

“The amount of water needed for salmon restoration is way below the flood stage,” said Dave Koehler, director of the San Joaquin River Parkway and Conservation Trust.

Nevertheless, farmers are concerned that over time — as more and more water is released at Friant Dam — water could start to seep into their fields and cause just as much damage as flooding.

“The water won’t go over the top [of the river banks], it will just go right through — like a sponge,” said Randy Houk, a farmer who is also owner and general manager of the Columbia Canal Co. in western Madera County.

Jason Phillips, river restoration program manager for the Bureau of Reclamation, said his agency has been examining the issue for years and is well-prepared to address any problems that may arise. He acknowledged, however, that crop damage from seepage is “a significant concern.”

“We’re taking it very seriously,” Phillips said.

Farmers in some parts of western Fresno and Madera counties are especially worried about seepage because their land has shallow aquifers with less room for water storage — which means areas beneath their fields could be flooded more easily.

The Bureau of Reclamation hasn’t specified exactly how it will stop seepage, although Phillips said the bureau has installed a series of monitoring wells that will let officials know whether water levels have risen too high.

Steve Chedester, director of the San Joaquin River Exchange Contractors Authority, which represents west-side farmers along the rivers, said the Bureau of Reclamation needs to do everything it can to make sure seepage won’t occur.

According to the settlement agreement that created the project, the river’s restoration is not supposed to harm crops, Chedester said.

Jose Antonio Ramirez, city manager in Firebaugh, which abuts the river, said he expects the additional river flows will result in more lush vegetation along the river’s edge. If too much water is released, however, the underground water level could rise, making it difficult to dig foundations for construction projects, he said.

Ramirez said that as the river restoration continues and water flows increase, he doesn’t believe his town will be in any more danger of flooding than in prior years — thanks in large part to channels that help control flooding.

In April 2006, high waters from the Kings and San Joaquin rivers threatened to flood Firebaugh — and townspeople scrambled to protect their homes with sandbags — but enough water was diverted to avoid disaster.

“Even if we had a doomsday event — someone blew up the dam and all the water came out — it would never flood Firebaugh,” he said.

The Federal Emergency Management Agency said it has no plans at this point to change flood insurance rates as a result of the river restoration project.

Downstream from Firebaugh, there are a handful of structures — including at least one house — that someday may be at risk of flooding because they are in the river’s direct path. One home was built in 1979 a few miles northeast of Los Banos in a stretch of the river that has been mostly dry for decades.

Its owner, farmer Daniel McNamara, declined to be interviewed. But officials say they are aware of McNamara’s unique situation.

“We need to identify structures that would be impacted by the river, and that house would clearly fit into that category,” Phillips said. For now, that stretch of the river will remain dry. Instead, water will be diverted through a bypass canal.

But that may change in a few years, depending on how the restoration process goes, officials said. And if it does, McNamara would become a rarity in California — a farmer with too much water.

“That’s a major concern for him,” Chedester said.