The study of beta diversity and its turnover and nestedness components allows us to understand the mechanisms that structure biotic communities within an ecosystem, which in turn enables the creation of strategies for their conservation and management. This study analyzed the beta diversity of fish assemblages in a coastal lagoon from two diversity facets: taxonomic and functional. Six bimonthly samplings were conducted by dividing the lagoon into three zones (inlet, mixing, and upper). Three trawls were performed at random points within each zone, and the parameters of dissolved oxygen (DO), pH, total dissolved solids (TDS), salinity, temperature, and depth were determined. A total of 1437 fish were captured and identified, and 14 functional traits related to locomotion and feeding were determined. Additionally, the beta diversity and its components for each diversity facet were determined. Differences in physicochemical parameters between climatic seasons and lagoon zones were identified; the external zone showed a higher number of species. However, the mixing zone exhibited greater functional richness, indicating that species with different functional characteristics converged in this area. Functional beta diversity showed higher values than taxonomic beta diversity, demonstrating functional differentiation of fish in the lagoon. In both facets, the turnover component predominantly contributes to beta diversity. The correlation between diversity and physicochemical parameters suggests that an environmental filter determines the presence of certain species and functions within the lagoon.