Freshwater ecosystems are hotspots of microbial biogeochemical processes and both their biodiversity and function are currently threatened by global change. As the composition of microbial communities rapidly alters when subjected to environmental change, it is important to understand how these structural changes translate into functional changes. To achieve this deeper understanding, this research project will study the observable (phenotypic) and genome-imprinted (genotypic) properties of individual bacterial cells, and associate these with the function and genomic adaptations of bacterial populations in freshwater ecosystems. We focus on the world’s largest freshwater ecosystem, the Laurentian Great Lakes, which has been altered significantly due to global change, with unknown impacts on its bacterial community. Our approach consists of integrating phenotypic information acquired through flow cytometry with genotypic information assembled from single-cell sequencing. This data integration will lead to a detailed understanding of how phenotypic and genotypic properties are related in the environment, how bacterial populations change their phenotypic properties in the environment, and how phenotypic populations contribute to ecosystem functioning. Ultimately, this knowledge will enable us to implement flow cytometry-based models as fast, cost-efficient tools for managing freshwater ecosystems by steering them towards microbial communities with desired functional traits.