Funding for the cleanup that began in 2008 was due to end this year, but Harper is committing federal support for another five years.
The second phase of the Lake Winnipeg Basin Initiative is to focus on projects and research to improve water quality for the fishing industry as well as for recreational users.
Harper threw cold water on any suggestion his government might reverse its decision and support another environmental water project it has already put on the chopping block.
The Experimental Lakes Area in northwestern Ontario is a project that has helped researchers for decades as they try to understand how freshwater bodies are damaged and how they can be restored. It started in the 1960s to study algae blooms choking Lake Erie.
The government is cutting its funding for the project, which is monitored by a team of scientists at the Freshwater Institute in Winnipeg.
"Our priority in this area is this particular project (Lake Winnipeg) and obviously we are not intending to continue that other project," Harper said.
Manitoba Liberal Leader Jon Gerrard and other supporters of the Environmental Lakes Area said ending the project also undermines research on Lake Winnipeg, where algae blooms are a major problem.
Harper said because more than half the pollution that enters the lake — much of it from fertilizer-laden agricultural runoff — comes from outside Manitoba, it is necessary to work with other jurisdictions to deal with it.
"This kind of scientific research is important for the long-term prosperity of our economy."
The hot TV lights at Harper's news conference in Gimli, Man., were too much for one young white-coated researcher, who collapsed after standing for more than an hour waiting for the prime minister to conclude.
She seemed to recover quickly and was ushered out of the conference room where Harper was speaking.
A handful of protesters yelling "Stop Harper" were outside the hotel where Harper made the announcement.
On another issue, Harper said he would be happy to talk with the Manitoba government about ways to prevent damage from flooding so as to minimize huge compensation payouts each year.
The province has complained that Ottawa has been slow to provide compensation under the federal disaster assistance program for last year's major flood.
Later in the day he travelled to a cowboy-themed banquet hall just north of Winnipeg called the Hitch’n Post Ranch where he extolled the virtues of his Conservative government at a party barbecue.
Almost 800 Conservatives sat under the shade of a tent or stood in the sun to hear him tell the world it should be a little more like Canada.
"I'm determined that Canada will continue to outperform Europe, the United States and Japan and that we will not fall into the long-term difficulties that those economies are facing," he said.
He drew one of the biggest responses from the crowd when he reminded them that his government had finally kept its promise to eliminate the long-gun registry.