All vessels equipped with an on-board toilet will soon be forced to install sewage tanks or marine sanitation devices, according to Transport Canada.
The requirement has been law for seven years, but Ottawa granted a reprieve for fishing and pleasure boat owners because of the cost of installation.
Transport Canada manager Paul Topping said government will work with boat owners who cannot afford to meet the deadline.
"In the case of someone who is a fisherman and who is genuinely trying, but may have some challenges, we take that into consideration. If it's someone who has means but is not complying with the [regulations] deliberately, that's a different story," said Topping.
Topping said government is trying to find a way to get people to follow the rules, without causing too much struggle for boat owners.
"It's not our intent to cause undue hardship to those members of the community, but we do want to see compliance with our regulations, so we are trying to develop an enforcement approach that will balance both those needs," he said.
Transport Canada will start enforcing the rules as of May 1.