Ephemeral wetlands are globally important systems that are regulated by regular cycles of wetting and drying, which are primarily controlled by responses to relatively short-term weather events (e.g., precipitation and evapotranspiration). Climate change is predicted to have significant effects on many ephemeral wetland systems and the organisms that depend on them through altered filling or drying dates that impact hydroperiod. To examine the potential effects of climate change on pine flatwoods wetlands in the southeastern United States, we created statistical models describing wetland hydrologic regime using an approximately 8-year history of water level monitoring and a variety of climate data inputs. We then assessed how hydrology may change in the future by projecting models forward (2025-2100) under six future climate scenarios (three climate models each with two emission scenarios). We used the model results to assess future breeding conditions for the imperiled Reticulated Flatwoods Salamander (Ambystoma bishopi), which breeds in many of the study wetlands. We found that models generally fit the data well and had good predictability across both training and testing data. Across all models and climate scenarios, there was substantial variation in the predicted suitability for flatwoods salamander reproduction. However, wetlands with longer hydroperiods tended to have fewer model iterations that predicted at least five consecutive years of reproductive failure (an important metric for population persistence). Understanding potential future risk to flatwoods salamander populations can be used to guide conservation and management actions for this imperiled species.