Understanding how bird populations respond to changes in waterbody availability in the climatically variable Prairie Pothole Region (PPR) of North America hinges on being able to couple hydrological and climate modeling to represent potential future landscapes. Model experiments run with the Pothole Complex Hydrologic Model using downscaled climate data (variables relating to precipitation, temperature, and potential evapotranspiration at 1/8° spatial resolution under four general circulation climate models and two gas emissions scenarios) were used to forecast the abundances of six focal wetland‐dependent bird species in the Missouri Coteau portion of the PPR, providing ensemble scenarios at a spatial scale relevant to resource management. Although the projected number of May ponds (waterbodies present during bird breeding season) fluctuated through time with some decadal periodicity (and with the number present in a given year reflecting abundance over the previous three years), the ensemble model average indicated an increase in the average number of waterbodies present by the turn of the next century. Overall, the model experiments conservatively projected an 11.75% increase in the number of waterbodies present by 2090–2099 compared to a baseline period from 1967 to 2005 in the PPR. Wetland‐dependent bird occurrence and abundance were significantly associated with temporal patterns and decadal periodicity in waterbody dynamics. Because of the strong associations between wetland‐dependent bird occurrence and abundance and the number of prairie potholes, projected waterbody increases are forecasted to result in an 11.97% overall increase in occurrence and 8.63% increase in abundance of the six focal species by the end of the 21st century; these results contrast with forecasted drought‐associated declines in waterbodies and birds in the PPR. This integrated hydrological–climatological approach offers a means of assessing how wetland‐dependent bird populations may respond to changes in wetland habitat availability due to a changing climate. Our results provide information that can help managers decide how to mitigate the effects of climate shifts on the distribution of wetland habitat and biota.