The East Kootenay Integrated Lake Management Partnership (EKILMP) is a coalition of various agencies, local governments, First Nations and non-government organizations with joint responsibilities to protect lake ecosystems. The mandate of the partnership is to maintain the integrity of lake ecosystems for fish, wildlife, drinking water, heritage, recreation and aesthetic values. EKILMP develops science-based, coordinated management guidance for land and water uses associated with East Kootenay lakes, in southeastern British Columbia. WindermereLake was chosen as the pilot study lake due to the presence of a highly motivated local water stewardship group, Wildsight and their Lake Windermere Project, heavy development pressures, high fish and wildlife values, ongoing land use planning processes and source water issues. Results show that 62 percent of WindermereLake’s shoreline is classified as disturbed. Anthropogenic alterations include the construction of foreshore structures, riparian vegetation removal, wetland infilling and modifications of the land base, including the construction of roadways and the railway. The Sensitive Habitat Inventory Mapping (SHIM) documents land use, water quality, fish and wildlife values, riparian and wetland habitat changes and identifies sensitive areas requiring protection. SHIM and a scientifically defensible Aquatic Habitat Index provides a cumulative impact assessment that will guide development and provide opportunities for conservation, enhancement and restoration initiatives. The Partnership identified areas on Lake Windermere that are essential for the long term maintenance of fish and/or wildlife values through both the Habitat Index Analysis process and the Zones of Sensitivity analysis. These areas include most tributary outlets, wildlife corridors, contiguous wetlands, in-lake wetlands, natural grasslands, cliff/bluffs, important gravel/cobble areas used by burbot or other species for spawning/rearing and areas of high productivity such as mussel beds. It also includes remnant natural areas. EKILMP recommends that these areas be designated for conservation use, and that no development occur within them. Low impact water access recreation and traditional First Nation uses are permissible in these areas, but permanent structures or alteration of existing habitats is considered to be unacceptable. The Partnership also identified shoreline areas where low impact development could occur, areas where development with normal constraints (ie current guidelines) could occur and areas where redevelopment with restoration would benefit the long-term health of the lake. SHIM results assist managers, planners and communities in land-use planning, development of regulations, standards and policies, leading to improved scientific knowledge as the basis for decision-making.