A contrast in the 87Sr/86Sr ratio of atmospherically derived Sr (∼0.710) and Sr from regional bedrock (>0.730) allows quantification of the proportions of precipitation recharge and groundwater discharge into peat columns of bogs and fens in the Glacial Lake Agassiz Peatlands. Two contrasting bog-fen pairs were studied: The Lost River peatland located over a regional groundwater discharge zone and the Red Lake peatland situated atop a hydrologic divide where recharge is expected to occur. Bog pore waters consist of 90-100% precipitation in the upper 2 m, below which they mix with groundwater. Adjacent fens consist mostly of groundwater, ranging from ∼30% near the surface to ∼100% with depth. At the Red Lake peatland, mixing relations suggest an additional Sr source that may be peat mineralization. Distinct 87Sr/86Sr and [Ca]/[Sr] ratios for groundwater discharging into bog and fen sites are indicative of distinct groundwater sources and are likely indicative of flow paths at two different length scales.