El Soldado is a semi-arid subtropical coastal lagoon subject to ecological conservation in the Gulf of California, where we reviewed the changes in the fish community structure before (1972; 1978–79; 1990–92) and after (cycle 1, 2018–2019; cycle 2, 2019–2020) the decree as a protected area, and we determined spatio-temporal changes between two consecutive annual cycles. We conducted monthly fish sampling cycles 1 and 2 with a small trawl net at three sites, where water and sediment variables were recorded, and drift macroalgae biomass was estimated. Results showed 99 fish species have been recorded in previous studies, and our study added 11 species. The fish assemblage (2018–2020) comprised 34 marine species and nine of them were dominant in both cycles. In general, higher fish abundance, richness, and diversity were observed in the cycle 1. Spatial changes, in both cycles, showed higher fish abundance, richness, and diversity in the innermost area of the lagoon, characterized by silty sediment and higher drift macroalgae biomass. Temporal changes showed higher fish abundance, richness, and diversity in summer-autumn during cycle 1, while during cycle 2, the higher values were in winter-autumn, mainly associated with seasonal variations in water temperature and the biogeographic affinity of fish species, but were also attributed to changes in the density of species classified as dominant. There was notable a drastic decrease of fish richness, diversity, and density during summer in cycle 2, which was attributed to be a warmer year. El Soldado fish community showed changes before and after the decree as a protected area, but also in the contiguous cycles. These changes include the addition of species, the prevalence of common species over 48 years, and the current dominant species that belong to indicator groups, which exhibit effectiveness in the conservation of this ecosystem.