For first phase of the LWBI (2008-2012), Canada and Manitoba signed a Memorandum of Understanding (MOU) on long-term collaboration to improve the health of Lake Winnipeg. The first phase funded research to investigate water quality issues within the lake and its watershed. Through these efforts, the initiative was able to fill important gaps in research, data collection and monitoring of the lake's ecology and sources and movement of nutrients that contribute to the large and persistent algae blooms seen in recent years.

Phase I included funding Sensitive Habitat Inventory and Mapping (SHIM) along the South Basin of Lake Winnipeg, a project of the Lake Winnipeg Foundation.

Phase II of the LWBI (2012-2017) will build on scientific accomplishments of Phase I and will move towards taking greater action to address water quality issues, including:

• Targeting the stewardship program to areas that need funding the most, on actions with the best possible impact on water quality.
• Greater watershed research and monitoring.
• Increasing collaboration between government watershed partners to develop nutrient-reducing agreements.