But he said he has no intention of restoring funding for the Experimental Lakes Area, a research facility that is being cut off from federal support.
Federal funding for the Lake Winnipeg Basin Initiative, a project that began in 2008 and was due to end this year, will continue for the next five years, Harper announced at an event in Gimli, Man. About $18 million is being committed to the project, he said, bringing the total so far close to $40 million.
"We're seeing positive results but more needs to be done," Harper said.
Harper said the federal government will work with the Lake Winnipeg Research Consortium to combat the growth of nutrients in the lake that has led to massive algal blooms in recent years because of high phosphorus levels. Algal blooms are known to create aquatic dead zones, kill fish and pose risks to other wildlife, and they can make the lake water toxic and dangerous if ingested.
"Actions that will improve the quality of Lake Winnipeg and the life and livelihood she supports will be a priority," he said.
The prime minister said the lake is not only important environmentally, but also economically. The tourism industry will benefit from cleaner water in the lake because more beaches will open, other recreational activities will increase, and the commercial fishery at the lake, currently worth $50 million per year, will also get a boost, he said.
Harper said scientists have found that at least half of the toxic nutrients in the lake are coming from outside of Manitoba and the large watershed has meant working with four U.S. states and four provincial governments to clean it up.
Protesters attend Harper's announcement
"We have ambitious goals for Lake Winnipeg, and so we should," he said. "We have a great deal of work still to do on this project but I'm confident that we will do it and do it well."
Public Safety Minister Vic Toews, a Manitoba MP, local MP James Bezan and a number of other members of the Conservative caucus joined Harper for the announcement at a hotel and resort on the shore of Lake Winnipeg.
Protesters were also at the site to confront Harper over cuts to the Experimental Lakes Area (ELA), a series of lakes in northwestern Ontario where scientists have produced world-renowned research. Their studies have included the effects of acid rain and phosphates on freshwater lakes, such as Lake Winnipeg. The government announced in its most recent budget it was ending about $2 million in annual funding for the ELA effective this fiscal year.
Harper was asked about the ELA and he made it clear the government has no intention of reversing its decision to close the facility. He said his government has increased funding for environmental scientific research, and research generally, even during the current period of fiscal restraint.
"Obviously there's important environmental needs here but generally speaking this kind of scientific research is important for the long-term prosperity of our economy," he said. "These research priorities will evolve over time. Our priority in this area is this particular project and obviously we're not intending to continue that other project."
But the ELA supporters say closing the research centre will "devastate" the scientific community's ability to find solutions for Lake Winnipeg's problems.
"Funding Lake Winnipeg research without funding ELA is like sending rowers to the Olympics without oars," said Jon Gerrard, Manitoba's Liberal leader, in a press release. He attended Harper's announcement in person.
The ELA is at the forefront of understanding the blooms of algae that plague Lake Winnipeg every summer, the advocates say, and its past research led to the removal of phosphorus from detergents and improved water quality in lakes around the world.
ELA scientists have helped train the scientists who work in Manitoba, they added, and cancelling the funding for the centre is detrimental to the health of all Canadian lakes they argue.