Environmental impacts of oil spills are a major public concern, impeding social license for the development of the petroleum sector and Canada’s economic development. Furthermore, there is uncertainty around the best methods to employ when cleaning oil spills in sensitive freshwater ecosystems. The International Institute for Sustainable Development-Experimental Lakes Area (IISD-ELA) has begun a large, collaborative, and multi-phased program to: a) determine the effectiveness of non-mechanical and biological methods for cleaning spilled oil from freshwater aquatic environments, and b) develop non-lethal and minimally invasive monitoring techniques to measure oil exposure and recovery in aquatic wildlife populations. The FLOWTER project builds upon this program in order to i) optimize Engineered Floating Wetlands (EFWs) to enhance the associated rhizome microbiome to achieve rapid oil degradation, and ii) validate fin clips and mucus swabs as non-invasive biological assessment tools for monitoring cleanup performance. More effective treatment and monitoring of oil spills are expected to increase social license and regulatory approval for oil infrastructure, which could add an estimated $3.2 billion to Canada’s gross domestic product. These optimized tools will also benefit industry and Canadians by significantly reducing response costs, follow-up resource and property damage claims, and by restoring ecosystem services more quickly.