Global sea level rise and increased storm activity triggered by climate change pose a serious threat to low-lying Arctic coastal landscapes, which commonly host numerous freshwater lakes. Marine inundation of these ecosystems would result in significant ecological changes. We elucidated effects of changing levels of marine influence to lake ecosystems by exploring the ontogeny of coastal Greiner Lake in Arctic Canada. Using paleolimnological methods on a sediment core, we explored functional assemblage compositions of aquatic biota (diatoms and chironomids), biomarkers (pigments and fatty acids) and geochemistry (stable isotopes and organic matter) throughout the isolation history of the lake. The biological and geological data collectively indicated a paleoenvironmental shift from marine embayment to brackish lagoon in the Late-Holocene and to a freshwater lake ca. 500 BP. We observed that the lake was most productive during a phase of mixed freshwater and marine influence, based on higher chlorophyll-a and β,β-carotene concentrations, omega-3 fatty acids (ω-3) as well as sediment organic content. We suggest that, in addition to reorganization of aquatic communities and altered ecosystem services provided by coastal lakes, coastal freshwaters may become more productive under increasing marine influence caused by climate change. Global sea level rise may thus trigger a new pathway to increasingly greener Arctic.