Mercury concentrations ([Hg]) in fish reflect a complex array of interacting biogeochemical and ecological variables. In northern regions where fish are a critical subsistence food, understanding and predicting fish [Hg] can be particularly difficult, largely due to a paucity of comprehensive data associated with the logistical challenges of field sampling. Building on previous work where we elucidated causal relationships between fish [Hg] and a variety of catchment, water quality, and ecological variables in subarctic lakes, we investigated whether using only ratios of catchment area to lake area (CA:LA) can predict [Hg] in northern freshwater fish species. As CA:LA can be sensed remotely, they may be more feasible and practical to obtain than field data in far northern regions. Our study included thirteen remote lakes that represent a CA:LA gradient of 6.2–423.5 within an ∼66,000 km2 subarctic region of Northwest Territories, Canada. We found that size-standardized [Hg] in three widespread fish species, including Lake Whitefish (Coregonus clupeaformis), Walleye (Sander vitreus), and Northern Pike (Esox lucius), were significantly and positively related to CA:LA (p < 0.007, r2 = 67–80%), indicating higher fish [Hg] in smaller lakes surrounded by relatively larger catchments. Our findings provide compelling evidence that remotely sensed CA:LA can be used to predict [Hg] in northern fishes and aid in prioritizing understudied and subsistence fishing lakes of the Canadian subarctic for [Hg] monitoring programs.