Salt pans are unique wetland ecosystems. In the Austrian Seewinkel region, salt pans are in an increasingly vulnerable state due to groundwater drainage and heightened climatic pressures. It is crucial to model how seasonal and long-term hydrological and climatological variations affect the salt pan dynamics in Seewinkel, yet a comprehensive understanding of the driving processes is lacking. The goal of this study is to develop random forest machine learning models driven by hydrological and meteorological data that allow us to predict in early spring (March) of each year the inundation state in the subsequent summer and fall. We utilize Earth observation data from Landsat 5 (L5), 8 (L8), and 9 (L9) to derive the time series of the inundation state for 34 salt pans for the period 1984–2022. Furthermore, we demonstrate that the groundwater level observed in March is the strongest predictor of the salt pan inundation state in summer and fall. Utilizing local groundwater data yields a Matthews correlation coefficient of 0.59. Models using globally available meteorological data, either instead of or in addition to groundwater data, provide comparable results. This allows the global transfer of the approach to comparable ecosystems where no in situ data are available.