Fish assemblages change significantly with physical and chemical characteristics of water; however, their response to the variability of geomorphic habitats has been rarely evaluated in lagoon-estuarine in one of these systems of the Mexican Pacific. Spatio-temporal variation of fish assemblage structure was assessed for three habitats: lagoon, estuarine, channel and inlet. The hypothesis was that sheltered areas support comparatively higher richness and abundance of fish species, with more small-sized specimens than the most exposed areas. We found that the ichthyofauna differed significantly among habitats. Several species were smaller in the lagoon compared with the other habitats, suggesting a use of the lagoon as a nursery ground. Moreover, dominant species for the lagoon were rarely found or absent in the inlet, whereas others were found only present or with higher abundance in the inlet. Although seasonal differences in richness and composition were detected, the evidence of fish-habitat associations for many species was noticeable regardless of seasonality, probably due to a high percentage of resident species during the annual cycle. The lagoon supports a greater abundance and species richness, due to a more sheltered and structured habitat, evidencing habitat-driven segregation in fish assemblages, and an aspect that should be incorporated for management of coastal ecosystems.