Calcareous fens are peat-accumulating wetlands fed by calcium-rich groundwater that support several threatened species of plants that thrive in these geochemical conditions. This investigation characterized the hydrology of two calcareous fens in the Glacial Lake Agassiz beach ridge complex in northwestern Minnesota, USA. Sandy surficial beach ridge aquifers and underlying buried glacial aquifers were considered as sources of groundwater to the fen. A combination of the two sources influenced by seasonal hydrology was also considered. Synchronous hydrologic responses to rainfall events and hydraulic gradients indicate the calcareous fens are well-connected to the beach-ridge aquifers. Chemistry of water discharging to the fens is calcium-magnesium-bicarbonate type similar to the beach ridge aquifers, and distinct from buried aquifers that have significant sodium and chloride. High tritium values and oxygen isotope signatures similar to the beach ridge aquifers characterized fen water. Beach ridge aquifer complexes are relatively thin (8–10 m) and overlie thick clay/clay loam till. These beach ridges exhibit high seasonal recharge and have permanent saturated zones, providing a continual source of calcium-rich water for the fens. Electrical resistivity profiles characterized the glacial stratigraphy and highlighted the well-developed physical connection between beach ridge aquifers and calcareous fens. The results of this study allow evaluation of the potential impacts of irrigation and aggregate quarrying on calcareous fens along sand and gravel beach ridges.