Hotspots are priority marine or terrestrial areas with high biodiversity where delineation is essential for conservation, but equally important is their linkage to the environmental policies of the overall region. In this study, fish diversity presences were linked to abiotic conditions and different habitat types to reveal multi-species and hotspots models predicted by ecological niche modelling methods within the Bay of La Paz, Mexico (south of Gulf of California). The abiotically suitable areas for 217 fish species were identified based on historical (1975–2020) presence data sets and a set of environmental layers related to distances from mangroves and rocky shores habitats, marine substrate, and bottom geomorphology conditions. Hotspot model distribution was delineated from a multi-species model identifying areas with ≥60 species per hectare and was compared to the marine conservation areas such Balandra Protected Natural Area (BPNA), illustrating how these models can be applied to improve the local regulatory framework. The results indicate that (1) there is a need for the BPNA to be enlarged to capture more of the delineated hotspot areas, and thus an update to the management plan will be required, (2) new conservation areas either adjacent or outside of the established BPNA should be established, or (3) Ramsar sites or other priority areas should be subject to legal recognition and a management plan decreed so that these vital habitats and fish diversity can be better protected.