Environment Minister Peter Kent and Lisa Jackson, administrator of the U.S. Environmental Protection Agency, signed the updated deal in a brief ceremony in Washington on Friday.
The amendments address problems with invasive aquatic species, habitat degradation and the effects of climate change.
They also support continued work on existing threats to health and the environment in the Great Lakes Basin such as harmful algae, toxic chemicals and shipping discharges.
The updated agreement also calls for developing plans to protect and restore near-shore areas, the primary source of drinking water for Great Lakes communities and the area where most commerce and recreation occurs.
It agrees on the need to develop conservation strategies to protect native species and restore habitat.
The agreement says phosphorus-reduction targets for Lake Erie should be drafted within three years and it sets a two-year deadline for the development and implementation of an early detection and rapid response system for invasive species.
The original Great Lakes Water Quality Agreement was signed in 1972 and was last amended in 1987. The agreement committed the two countries "to restore and maintain the chemical, physical and biological integrity of the waters" of the Great Lakes and the portion of the St. Lawrence River that includes the Canada-United States border.
Kent and Jackson said the changes signed on Friday underline a commitment by both governments to improving the environment of the region. They said protecting the lakes will benefit millions of people who live on their shores in both countries.
"The 2012 Great Lakes Water Quality Agreement will provide renewed guidance for the restoration and protection of a precious natural resource,"Kent said.
"And it will help us, together, to work towards our ultimate goal: preserving the Great Lakes for present and future generations of Canadians and Americans."
He said the lakes partnership is a cornerstone of the relationship between Canada and the United States.
"We’ve shown that, by working together, we can make a difference."
Great Lakes United, an international conservation group dedicated to protecting the lakes, welcomed the amendments, but warned that the real work still lies ahead.
"This is only the first step," said John Jackson, interim executive director of group. "No matter what the words on the page say, this agreement will only be effective if the U.S. and Canadian governments act to implement it."
He said the changes took eight years to negotiate.
"We hope they will lead to revitalized action from the governments and their partners working together bi-nationally across the entire Great Lakes-St. Lawrence River basin from Duluth to Quebec City.
"Protection, cleanup and restoration are essential to ensure that we live in a vital, thriving Great Lakes basin. Today we applaud. Tomorrow we get to work."