Thermally induced coral bleaching is a major cause of reef decline, though it could be offset by coral adaptation. Here we used three complementary approaches to identify which environmental gradients drive local adaptation in two common Florida corals, Porites astreoides and Agaricia agaricites. Depth is the most important factor for both species: each contains three genetically distinct lineages segregated by depth. Additionally, each lineage harbors genetic variation aligning with other environmental gradients, though elevated temperature is typically not one of them. In A. agaricites, nitrogen variation predicts genetic divergence in the deep and mid-depth lineages, while cold temperature is the most important driver within the shallow lineage. Nitrogen and cold are also associated with genetic variation in P. astreoides, and high temperature was highlighted only once in the deep lineage of P. astreoides. In both species, lineages don’t share environment-associated groups of SNPs, indicating that lineages adapt independently. Overall, the locally available genetic variation in our two corals species seems unlikely to provide thermally adaptive genetic variants for future warming. Our results map the environmental gradients that create the strongest genetic barriers for corals, which could serve as a guide for reef restoration.