The action came at 10:45 p.m. after a 12-hour meeting in Rancho Cordova.
"No doubt it's going to cost a lot of money, but the Delta is worth it," said Pamela Creedon, executive officer of the Central Valley Regional Water Quality Control Board, which adopted the rules by unanimous vote.
Stan Dean, district engineer of the Sacramento Regional County Sanitation District, said appealing to the State Water Resources Control Board "is a very strong possibility."
It was Sacramento against the state during the meeting, at which about 300 people assembled to debate whether the capital should do a better job of treating its sewage.
Wastewater from the region's 1.3 million people is suspected of disrupting the ecology of the Sacramento-San Joaquin Delta. Because the Delta supplies drinking water for 25 million people, the meeting drew politicians and water agency officials from throughout the state.
The meeting continued into the night as competing parties debated obscure but important technical issues governing the proposed permit.
The meeting's morning session was dominated by competing dramatic claims by the participants, from Sacramentans who fear economic harm, to Southern Californians worried about their water supply.
"It is a war between North and South," Sacramento Mayor Kevin Johnson told the water board, in the day's first dramatic flourish.
State Sen. Bill Emmerson, R-Hemet, who represents Riverside County, countered that the Sacramento region can't ignore its environmental impact on the Delta.
"This isn't a North and South issue. This is a state issue," he said. "The Sacramento region needs to do its share."
The Sacramento Regional County Sanitation District discharges the region's wastewater into the Sacramento River at Freeport.
It must obtain a new discharge permit every five years under the federal Clean Water Act. The current permit dates to 2000, because the highly technical and controversial nature of the issue has caused delays.
The new permit would drastically reduce discharge limits for a number of pollutants. The central issues involve ammonia and cryptosporidium, an infectious pathogen.
Much of the argument Thursday centered on the cost of compliance. Sacramento officials have estimated that current sewage bills for a half-million customers would have to triple – to $60 a month – to pay for treatment plant improvements.
"Now is not the time," said Elk Grove resident Ted Benjamin. "Maybe it's right. But I cannot afford it."
Central Valley water board staff summarized years of evidence gathered on Sacramento's wastewater. The debate came down to three issues: ammonia, pathogens and oxygen depletion in the Delta's waters.
Recent studies have found problems in all three areas.
Ammonia in the region's effluent, for instance, is interfering with the reproduction of copepods, tiny phytoplankton at the base of the food chain. It also may have long-term health effects on the endangered Delta smelt.
Sacramento's sewage puts 14 tons of ammonia into the Delta every day, 99 percent of the total, according to the board's research. It's enough to cause toxic effects on test organisms all the way downstream to Rio Vista, about 30 miles away.
Water board staff also presented research, by University of Arizona assistant professor of biology Charles Gerba, that swimmers downstream from Sacramento's sewer outfall are twice as likely to get sick as those upstream.
"We are required to protect the ecosystem, and we know there are impacts now," said Ken Landau, assistant executive officer of the Central Valley water board. "I cannot emphasize too strongly, the science behind this is sound."
Numerous other officials support those conclusions and the proposed pollution limits, including the U.S. Environmental Protection Agency and California Department of Public Health.
The evidence, however, was disputed by a platoon of consultants hired by the Sacramento sanitation district. Some of the most persuasive testimony came from the district's expert on biology, who said there's no evidence the decline in copepods actually affects fish or the ecosystem.