The $390 million tunnel, which is scheduled to officially open Wednesday after nearly a decade of construction, will carry sewage through 24-foot diameter pipes before discharging the waste nearly 10 miles at sea.
Currently, the treated sewage is dumped several hundred feet off a treatment plant in Boston Harbor.
The discharge to the ocean will be at least 85 percent pure water because of primary and secondary treatment at the Deer Island plant in which solids are allowed to settle out of the sewage and bacterial and chemical treatment are used to clean it, said Jonathan Yeo, spokesman for the Massachusetts Water Resources Authority.
The pipe will carry an average of 320 million gallons a day, but is capable of carrying nearly four times that amount.
Opponents say the discharge could harm the marine ecosystem, but the water agency, which operates the tunnel, says federal guidelines and an aggressive monitoring system will limit the impact.
"I think the science program that has been built is probably the most comprehensive ever done," said Douglas B. MacDonald, the agency's executive director.
Critics say the money could have been better spent in finding a more effective way to treat waste water and fear the water agency will become less concerned about what gets dumped into the sewers.
"We should have spent the money on treatment, rather than transportation," said Mary Loebig, co-founder of the Cape Cod-based Stop the Outfall Pipe, which tried to halt the project. "I'm really angry that we're still using the same solutions when I was a kid that never worked."
Three workers have died since construction on the concrete-line tunnel began in 1991, and problems drilling through the undersea rock bed delayed the original completion date.