Millions of internally drained wetland systems in the Prairie Potholes region of the northern Great Plains (USA and Canada) provide indispensable habitat for waterfowl and a host of other ecosystem services. The hydrochemistry of these systems is complex and a crucial control on wetland function, flora and fauna. Wetland waters can have high concentrations of SO2-4 due to the oxidation of large amounts of pyrite in glacial till that is in part derived from the Pierre shale. Water chemistry including δ18OH2O, δ2HH2O, and δ34SSO4 values, was determined for groundwater, soil pore water, and wetland surface water in and around a discharge wetland in North Dakota. The isotopic data for the first time trace the interaction of processes that affect wetland chemistry, including open water evaporation, plant transpiration, and microbial SO4 reduction.