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Sediment cores were collected under ice‐cover in late winter from three wetlands located along a subsurface hydrologic gradient within the Prairie Pothole Region of North America. Within each core, sediment porewaters were analyzed byin situvoltammetry for a suite of redox active species as a function of depth and revealed shifts in complex oxidation‐reduction dynamics related to ice cover in these wetlands. We observed a reduced sulfur boundary that is close to or above the sediment‐water interface (SWI) under ice cover. In contrast, the reduced sulfur boundary retreats several centimeters deeper in the sediments under ice‐free conditions. These findings are analogous to previous observations in shallow lakes that show anoxia at the SWI during ice cover but not under ice‐free conditions. Further, biogeochemical processes varied depending upon wetland type. During winter, sulfide levels in sediment porewaters in groundwater fed “flow‐through” wetlands were significantly lower than under ice‐free conditions. The converse applied to groundwater discharge wetlands where reduced sulfur concentrations in porewaters increased under ice cover. Decreases in ice cover extent and duration due to climate change coupled with profound landscape changes due to agriculture will affect the biogeochemical cycles of these wetlands and could lead to increased carbon emissions in the future.