We developed a floodplain inundation model to extract specific flood extent and depth parameters and combined these with vegetation land cover and historic flow data to quantify spatial habitat suitability and temporal hydrologic metrics that support Alligator Gar Atractosteus spatula spawning within a 257 km segment of the lower Guadalupe River, Texas, USA. We modeled nine flows across a range of flood frequency recurrence intervals from 257 m3s−1 to ~4997 m3s−1 and estimated the availability of suitable spawning water depths (0.2 to 2 m) and lateral connectedness between the river and suitable floodplain landcover types. We estimated the ages via otoliths of 95 Alligator Gar collected in the reach to determine the year that they were recruited into the system. We analyzed a total of 30 Indicators of Hydrologic Alteration flow metrics to examine how the spatially derived suitable habitats related to the temporal aspects of flow occurrence during the spawning season for the period of flow record April–July (1935–2020) and to the years spanning the recruitment data of the Alligator Gar (1981–2010). A non-linear relationship existed between suitable spawning habitat area and the flow regime, with the most habitat availability corresponding to the 10–20-year flood recurrence interval frequency with peak flows of 2057–3108 m3s−1, respectively. The Alligator Gar recruitment data indicated that six years provided high recruitment, which correlated with peak flows of ~5-year frequency with an available spawning area of ~9000 Ha, moderate recruitment years related to peak flows with ~3-year frequency with an available spawning area of 6000 Ha, and low recruitment years where spawning was likely to occur at least every other year with at least 2500 Ha of available spawning area. The results of this model support the development of legislatively mandated environmental flow standards for the Guadalupe River Basin, inform field-based efforts for collecting empirical and observational data on the species’ reproduction, and provide spatial and temporal information for designing conservation strategies for Alligator Gar.