Honolulu violated a federal wastewater discharge permit more than 4,000 times by failing to meet construction schedules for two key projects and exceeding bacteria limits, a federal judge ruled yesterday in a lawsuit by three environmental groups.

Four years of delays in building a disinfection unit at the Sand Island sewage treatment plant resulted in 1,578 of the violations, one for every day the project was late, U.S. District Judge David Ezra found.

Delays in building a sewage pump station on Hart Street resulted in 832 violations, Ezra ruled. Also, discharged effluent exceeded limits for enterococcus bacteria 1,603 times.

Ezra rejected additional claims that sought to calculate violations for discharging excess levels of two toxic chemicals used in pesticides — chlordane and dieldrin — and to count violations of a 2002 compliance plan.

The suit was filed against the city in 2004 by the Sierra Club, Hawai'i's Thousand Friends and Our Children's Earth Foundation. The case will now move to a penalty phase.

"We're very pleased," said plaintiffs' attorney William Tam. "This will put the city on notice that there is a federal judge looking over what they're doing, and that what may have occurred in the past is not acceptable any more."

The city could theoretically be liable for nearly $300 million in penalties, but it is more likely that the plaintiffs will seek strict compliance benchmarks or added environmental protection.

City officials have long characterized the suit as an unnecessary drain on resources.

"This administration has been working closely with federal and state officials to address long-standing challenges in satisfying the city's permit requirements," city environmental services director Eric Takamura said in a statement. "Sierra Club's pursuit of punitive measures against the city detracts from these important efforts and from a productive resolution of these problems."

The court dismissed five other claims in 2005, and the plaintiffs later dropped three more.

The city spent more than $3 million on attorneys to oppose the suit, and the City Council has authorized spending up to $4.2 million in total.

The discharge permit required the city to build the disinfection unit by 2002, but construction problems and a lawsuit delayed completion until 2006. Meanwhile, the cost skyrocketed from $60 million to $100 million. The cost of the pump station was not immediately available.

The disinfection unit is now fully operational, but it has not yet begun a yearlong monitoring period of continuous operation to prove its effectiveness. The city is negotiating with the U.S. Environmental Protection Agency over when the period should start and end.

Reach Johnny Brannon at jbrannon@honoluluadvertiser.com.