Taxonomic Diversity, Community Structure, and Ecological Recovery of Soft-Bottom Fish Assemblages in La Paz Lagoon (Gulf of California, Mexico)

La Paz Lagoon is a semi-enclosed coastal ecosystem in the southwestern Gulf of California that was historically affected by wastewater discharges and other anthropogenic disturbances. This study evaluated the taxonomic diversity and community structure of soft-bottom fish assemblages across two climatic periods (Neutral, 2016–2017, and La Niña, 2022–2023) using alpha (α), beta (β), and gamma (γ) diversity metrics together with taxonomic distinctness indices (Δ, Δ*, Δ+, and Λ+). Six bimonthly surveys were conducted during each climatic period at seven sampling stations. A total of 93 fish species, representing 65 genera, 33 families, and 17 orders, were recorded across the two climatic periods. Species richness exhibited marked temporal variation, reaching its highest value in April and its lowest value in March. Periods of reduced richness were associated with increased species turnover among stations. Taxonomic distinctness indices remained within the expected confidence limits, indicating a stable taxonomic structure despite historical anthropogenic impacts. Dominant species included Paralabrax maculatofasciatus, Diapterus brevirostris, Eucinostomus gracilis, Urobatis halleri, and Synodus scituliceps. Overall, the results indicate that the soft-bottom fish assemblage of La Paz Lagoon exhibits characteristics consistent with a stable and well-structured community. Multivariate analyses further identified water temperature as the principal environmental variable associated with community variation. Collectively, these findings support the hypothesis that La Paz Lagoon is undergoing ecological recovery and provide a robust ecological baseline for long-term monitoring, conservation, and ecosystem management.