Alligator Gars Atractosteus spatula historically ranged throughout the lower Mississippi River basin and in the coastal river basins of the Gulf of Mexico from Florida to Mexico, but they have now experienced population reductions or extirpations in many parts of their range. Hydrologic alterations of river systems leading to reduced river–floodplain connectivity are thought to be a main contributor to these declines. To better conserve and manage this species, it is important to understand how hydrologic processes influence floodplain connectivity and ultimately the recruitment success of Alligator Gars. Utilizing a one‐dimensional hydraulic model combined with high‐resolution digital elevation models, a high‐resolution floodplain inundation model for the middle Trinity River, Texas, was created. Available land use and vegetation data layers were overlaid to identify and quantify suitable Alligator Gar spawning habitat based on recently developed habitat suitability criteria. Finally, we used this model to estimate historic spawning habitat availability using a hydrologic time series analysis. These spawning habitat availability data were combined with hydrologic and water temperature data and correlated with historic Alligator Gar recruitment success using published year‐class strength data. Our results show that in the middle Trinity River Alligator Gar recruitment success was correlated with variables associated with spawning habitat availability from May to July. The multiple characteristics reflecting the extent, duration, and time that spawning habitats were available appeared to interact to produce exceptional Alligator Gar recruitment.