The Canadian Food Inspection Agency is worried about the safety of eating affected shellfish. (CBC)

A sewage overflow this week into the Charlottetown Harbour again closed sections of the West and North rivers popular for shellfishing.

The season for fishing quahog, a type of clam, opened last week on Prince Edward Island, but a two-kilometre section of West River has been off limits most of the summer.

That has left quahog fishermen scrambling to find alternate locations to catch the mollusks.

"The No. 1 priority is food safety," said John White of the Canadian Food Inspection Agency. "We want to make sure that whatever shellfish is being harvested is not going to make anyone ill."

Heavy rains flooding the sewer system and forcing it to discharge into the harbour and adjoining rivers caused this week's closure. It was the fifth such incident this summer.

When that happens, the CFIA recommends to the Department of Fisheries and Ocean that it close the affected areas.

Regular occurrence

"Those events happened a number of times and we'd have to post and patrol and tell fishermen they'd have to fish in a different area, and that's what's ongoing now," said Bobby MacInnis of the DFO.

The number of sewage discharges is not unusual this year. What has changed is the CFIA's response to such incidents. Until two years ago, it did not require cities to report discharges.

The CFIA is now paying much closer attention to the impact sewage has on shellfish because global concerns have risen about the safety of consuming shellfish caught in polluted waters.

"Shellfish, being filter feeders, can accumulate these things in their tissues, making them unsafe to eat," said White.

He added that heavy rains will continue to cause the sewer system to flood and that will continue to cause the CFIA to close the waters to fishing.

The CFIA said it will test the water next week and if it's clear, the rivers will reopen.