"We found out about the projects when it was too late to condition them," Carrigan said.
"We normally won't stop or delay a project, we will just put conditions for the work such as not to use leaky equipment or require that they replant vegetation that gets removed."
Carrigan said the water board has met with the Corps of Engineers to discuss compliance with the Clean Water Act, but without success.
"We had several conversations but ultimately we just disagree what the Corps is required to do under the Clean Water Act," Carrigan said.
The water board says the Corps of Engineers violated permitting provisions of the law, which give the board notice and time to enforce water quality rules.
In December 2012, the Corps of Engineers cleared vegetation along Haskell Creek, a tributary of the L.A. River in the Sepulveda Basin, and also and dredged and filled in the river, again without a permit, the water board says.
Sepulveda Basin is a 2,000-acre flood basin and wildlife reserve in the upper L.A. River.
The Corps of Engineers stopped working on that project after the Los Angeles Times reported on it.
In both cases, the water board says, the Corps of Engineers used heavy equipment to remove vegetation and did little "to mitigate the discharges of oil, grease and other pollutants into these waters of the United States."
The board expects to Corps of Engineers to continue breaking the law, as the Corps of Engineers operates six flood risk management facilities and about 34 miles of flood control channels and levees in Los Angeles County.
These "are just two examples of the Army Corps' practice of ignoring its statutory requirement to obtain the Regional Water Board's certification prior to conducting dredge and fill operations," the complaint states.
"Base[d] upon a history of non-compliance, it is clear these violations are continuing and will recur."
The Corps of Engineers said it does not comment on pending litigation.
The water board seeks declaratory judgment, an injunction and costs of suit.