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HUNTINGTON BEACH — Scientists who spent more than a year studying the causes of the mysterious bacteria that shut down the beach here during the summer of 1999 have identified two prime suspects: bird waste from a nearby marsh and sewage flowing from a sanitation outfall. 

The long-awaited report is the most exhaustive examination to date of the contamination problem that kept the famous “Surf City, USA” beach off limits for months, dealing a blow to Huntington Beach’s tourist economy. 

High bacteria counts were first recorded in June 1999, and the eight-mile beach did not completely reopen until September of that year. The cause of the bacteria remained a mystery, but a group of 11 scientists on Thursday presented what they considered their best theories. 

According to the scientists, birds living in the nearby Talbert Marsh produced waste with a strong strain of bacteria that “incubated” in the marsh and eventually washed into the surf. 

Meanwhile, the report says, the Orange County Sanitation District released partially treated sewage from an underwater outfall four miles off the coast. Normally such sewage stays away from the beach, but in this case warm water from a nearby power plant drew the effluent to the surface, polluting the beach. 

The $1.5 million study was funded by the sanitation district, Orange County and the city of Huntington Beach. It was spearheaded by Stanley Grant, an engineering professor at the University of California, Irvine. 

Now more study is needed to determine how to prevent the pollution from coming back, officials said. 

Indeed, scientists pointed out that the bacteria apparently caused by bird waste at the Talbert Marsh raises questions about whether the effort to protect such marshlands conflicts with the goal of clean ocean water. 

“Marshes have always been thought to be cleansers,” Grant said. “What this study showed was, surprise, they are not. That on the contrary, the water coming out has more bacteria than when it comes in.” 

Grant said he could think of no easy answers to prevent the bird waste bacteria from mixing with the ocean water. 

Not all findings in the report were unchallenged. The Orange County Sanitation District took issue with the scientists’ theory that effluent from the agency’s outfall contributed to this beach closures. 

“We don’t find the same conclusion to be true,” district spokeswoman Lisa Lawson said. “We will be doing further studies to see if this theory is acceptable or not acceptable.”