Understanding the spatial patterns of plant diversity across vernal pool complexes remains challenging, as plant communities change rapidly in time and concurrent collection of relevant data for modeling remain logistically elusive. In the absence of coupled ecohydrological data, we demonstrate that the application of drone-mounted light detection and ranging (LiDAR) systems to vernal pools enables estimation of species richness using hydrological proxies and spatial modeling. Parameters related to hydrologic connectivity, soil moisture, and hydroperiod describe substantial variation in species richness patterns (r2 = 0.28 ± 0.03) across vernal pool complexes. Converging factors, such as proximity to areas of hydrologic connectivity with low surface roughness, tend to promote forb richness but describe less of the variation in grasses. Estimates of species richness are accurate to within 2-3 species using models derived from UAV-LiDAR, providing an approximation of potential biodiversity hotspots in lieu of in-situ surveys.