Estuarine systems are highly productive ecosystems with diverse fish communities that provide valuable ecosystem services. The structure and ecology of fish communities in the estuarine systems of the Mesoamerican Barrier Reef System region (MBRS) is largely unknown. Here, the fish communities and their relationship with environmental variables were investigated for the first time in sixteen estuarine systems along the Honduran coast of the MBRS. The estuarine systems included estuarine lagoons and estuaries with different mouth dynamics, such as permanently open estuarine systems (POE) and temporary open-closed estuarine systems (TOCE). A total of 154 fish species were identified. Estuarine lagoons exhibited higher abundance and species richness, with Karataska and Chachaguala having the highest species richness (∼80 species). Overall, higher diversity was observed in POE systems and during the open mouth phase, likely due to higher dispersion rates. Fish species were classified into different functional groups based on their utilization of estuarine environments. The most abundant category was marine fish (50.6 %), with marine stragglers and marine estuarine-opportunists as the dominant guilds within this category. Freshwater, estuarine, and diadromous fish categories contributed less but similarly. Fish communities in estuarine lagoons and estuaries showed clear differences, although they shared some common species. Estuarine lagoons communities were dominated by the marine category and marine-estuarine-opportunists, while those of estuaries were characterized by the freshwater category and freshwater-estuarine-opportunists. The occupancy varied greatly, with some species present in multiple estuarine systems and others restricted to a single system. Species contribution to β-diversity (SCBD) revealed that species present in a single system made the greatest contribution. Local contribution to total β-diversity (LCBD) ranged between 1.48 and 20.10 %, with the Chachaguala estuarine lagoon being the main contributor. In addition to geomorphological features and estuarine mouth state, distance-based multivariate linear model (DistLM) showed that salinity, pH, bottom vegetation, and dissolved oxygen contributed significantly in explaining the fish metacommunity variation. This study shows the importance of environmental filtering in shaping local fish communities in the MBRS estuarine systems. However, further research is needed to understand the role of dispersion pathways and rates for the integral management of the estuarine fish metacommunity in the region.
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