When all of the water was released through the Seven Oaks Dam near Redlands in February, the rising river level down below was seen as good news for the Santa Ana sucker fish, a threatened species.
Environmental groups also applauded the government's decision to make parts of the Santa Ana River a critical habitat for the threatened fish, thereby off-limits to water companies.
But it's a decision the water companies are fighting, saying their customers have rights to the land as well.
"We don't even really know if the fish is in decline, and we'd like to know more about it before we start throwing water down the drain and costing our customers money," said Stacey Aldstadt, general manager, San Bernardino Municipal Water Department.
Aldstadt says not having access to the Santa Ana Riverbed will do much more than simply drive up the cost of water.
"The bigger impact, more than to just the customer's bill, is our ability as water agencies to provide for future growth," said Aldstadt.
But not everyone agrees with what the water companies are saying about the Santa Ana River. For example, one environmental group says the area needs to be designated a critical habitat.
"They're on a downward trend towards extinction," said Biologist and Public Lands Deserts Director Ileene Anderson, Center for Biological Diversity.
Anderson says unless the Santa Ana River is protected from the water companies, the sucker fish will suffer.
"It seems to me that instead of filing a lawsuit to try to challenge this critical habitat designation, that the water agencies should be proactively working to conserve the habitat for all of the benefits from water conservation that it brings," said Anderson.
As for the U.S. Fish and Wildlife Service, they say because of the active lawsuit, they have no comment.