Oyster fishing around Charlottetown has frequently been stopped this year. (CBC)

Charlottetown is going ahead with an $18 million sewage upgrade to prevent harbour pollution.

At a media conference Thursday afternoon, Mayor Clifford Lee said work will start this year and proceed in four phases through to 2014.

The province is contributing $6 million.

"All residents stand to benefit from the work, especially fisherman," said Robert Vessey, minister of public works. "When harbour closures are in effect, it greatly affects their industry."

Lee said the city will go $6.2 million into debt to pay for its share. City ratepayers will start paying for that immediately when their sewage bill goes up $30 a year as of April 1.

The city will also use $1 million a year from the gas rebate it gets from the federal government. The city hopes to recover more of the cost in 2014 via a federal infrastructure fund.

Lee said the tender for engineering work will be issued this month. He promised public consultation as the project proceeds.

The city's sewage system regularly overflows into the harbour. Part of the sanitary sewer system is combined with the storm sewer in the city. The treatment plant can't handle the excess volume in heavy rain so untreated sewage flows into the harbour.

The upgrade should stop that happening.

The problem has led to regular shutdowns of the shellfishery in the harbour, and the provincial public health office has recommended warning signs be posted for swimmers following heavy rains. Environment Canada ordered the city to make the fix last fall.

The P.E.I. Fishermen's Association and various shellfish groups applauded the announcement.

"It is going to clean up our harbour and it is an historic harbour," said oyster fisherman Stan Casey. "We can go back to work after this is cleaned up."