Canada’s watersheds are important natural resources, providing drinking water as well as water for agricultural, industrial and recreational uses. Growing demands from industry and populations are putting intense pressure on these freshwater systems. Recognizing this, the Canadian government and watershed stakeholders are adopting a new model of watershed stewardship called “source protection”. Using metagenomics, the research team looked at microbial communities to develop new tools to be included in Canada’s larger ‘source protection’ toolbox. The “Watershed Health Profile” tool measures a panel of microbial markers to quantify the health of the ecosystem and outputs a numerical value that can be incorporated into the Canadian Water Quality Index and can warn of potential threats to the various users of the watershed. The second tool, the “Microbial Pollution Profile” can be used to identify the specific source of fecal pollution in contaminated watersheds to be used by watershed managers as part of their pollution abatement and ongoing best practice monitoring efforts.