Wetlands densely populate the ecoregion transecting the center of the Prairie Pothole Region (PPR) known as the Missouri Coteau and epicenter to the most productive waterfowl-breeding habitat in North America. These palustrine, depressional basin waters vacillate with regional drought and deluge, so surface water fluctuations over time modulate wetland productivity, habitat, and water quality functions. Models predict formidable effects of climate change on glacial basin surface waters, yet large-scale, long-term observation data are lacking to compare against predicted changes. Current, optical-based water detection models do not delineate marsh vegetation from shallow, turbid, high-chlorophyll waters common to the region. We developed a palustrine wetland spectral model for tracking open surface waters using Landsat imagery, which we evaluated for a 2500 km2 landscape that estimates seasonal and annual open water variability for thousands of individual wetlands in the Missouri Coteau ecoregion. Detection accuracy of 96% was achieved for water bodies greater than a half-pixel in size. We identified shifts in the distribution of water permanence classes within and between years for waters emerging in spring, mid-summer, and late summer from 1997 to 2005 and identified a maximum of 19 047 basins with open water (12% of the landscape) populating 2500 km2. For the 2005 growing season, we observed only 8757 basins with open water (6% of the landscape) for the same area. Declines were greatest for water bodies detected only in spring, suggesting a loss of those wetlands functioning to recharge groundwater stores early in the season and a high sensitivity to observed reductions in snowfall. If landscape factors driving open water coverage and wetland density are similar for the entire Missouri Coteau, we estimate the number of basins containing at least a pixel of water for this region declined from 577 600 to 266 000 between 1997 and 2005.