Tide pools are important environments for several fish species, as they offer essential resources such as shelter and food. Thus, understanding the relationships of the ichthyofauna with the habitat structural characteristics in tide pools is important to understand the distribution patterns of fish assemblages in shallow environments. This study investigated how the habitat structure in tide pools influences the reef fish assemblages in Southwestern Atlantic (Bahia, Brazil). During 17 months, tidal pools were evaluated through visual censuses aiming to sampling the ichthyofauna, and additionally, variables of the structural characteristics of the pools (depth, area, volume, rugosity, etc.) were measured. By using multiple statistical modeling approaches, we found that there were significant differences in diversity, abundance, and species richness at the interaction between time and space factors, with higher averages of the three variables during the warmer months across all reef banks. Moreover, at local spatial scale, greater coral‐dominated and complex pools harbored higher fish species and diversity, while algae cover was most important in shaping fish numbers. The most important variables in the structuring of the fish assemblages were the pool volume, distance from the edge of the reef, and habitat complexity, confirming our hypothesis. Resident fish species were found in pools near the out reef edge, while occasional and transient species were found in pools closer to the inland sea. Our study highlights the multi‐scale role of habitat characteristics as predictors of the fish assemblage structure in these extremely variable environments and emphasizes the need to protect these fragile and overexploited tidal pools.