California rock pools are seasonal freshwaters that support several threatened and endangered species. They are a sparse and understudied habitat but important for biodiversity, endangered species, and endemic species. The endangered Longhorn Fairy Shrimp (LFS)(Branchinecta longiantenna) is found in rock pools, but little is known of its ecology. The purpose of this study was to assess LFS distribution and abundance as they are associated with numerous biotic and abiotic variables. Rock pools were sampled between November 2016 and May 2019 at sites in Alameda and Contra Costa counties. Since Vernal Pool Fairy Shrimp (VPFS)(Brachinecta lynchi) are common in rock pools, we also included it as a focal species in this study. Out of over 900 pools sampled, LFS occurred in 8% and VPFS occurred in 70% of the pools. Both species were influenced by hydrological patterns and associated with many pool characteristics (e.g., depth, exposure), abiotic (e.g., phosphates, conductivity) and biotic (e.g., competitors, predators) variables. Unoccupied pools were not significantly different than occupied pools. These results provide new insight for guidance on future management and the eventual recovery of these threatened and endangered species.