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Coastal transition ecosystems like estuaries are amongst the most productive aquatic ecosystems on the planet, recognized worldwide as a fundamental component of coastal areas in terms of biological relevance and anthropogenic use. Estuaries along the Portuguese coast differ in their geomorphological and hydrological characteristics. These systems play a crucial role in terms of nursery areas for economically important fish species. Although several authors have observed high specific variability in estuarine fish communities along the Portuguese coast, few studies explore the factors that influence it. Most of these studies focus on a single estuary and, when several are addressed, only a single factor is used to assess the specific variability of the communities. The presente work aims to analyze the ecological role played by these estuaries for fish communities, namely in terms of their species richness, using a 30 year historical database provided by the Portuguese Coastal Monitoring Network Research Infrastructure (CoastNet RI). To this end, a generalized additive model (GAM) was developed to analyze the variation of species richness as a function of a set of temporal, spatial and environmental characteristics from the nine principal estuarine systems on the Portuguese coast. A total of 142 species from 45 families were identified. The Tejo, Mira, and Sado estuaries had the highest species counts (92, 72, and 64 species, respectively), while Minho and Ria de Aveiro had the lowest (26 and 27 species, respectively). The GAM model explained 35.1% of the variance in species richness and demonstrated significant differences in fish species richness in space (among the nine study estuaries) and time (at annual and monthly scales), and these differences were influenced by abiotic factors such as salinity and temperature. Species richness decreased with higher latitudes and varied yearly, showing a downward trend post-2002. Monthly variations showed increases in February–March and September–October. Higher species richness correlated with salinity levels between 25 and 37 and temperatures between 14 and 25 °C. Possible scenarios of future variations caused by the effects of climate change on the significant factors are also discussed. These GAMs could be useful as a preliminary tool to prepare long-term conservation plans for national legislation. • Analyzing historical data provided by CoastNet collected in the last three decades. • 142 fish species belonging to 45 families were identified in the data compiled. • The model explained 35.1% of the total deviance for fish species richness variation. • Significant variables were: estuary; latitude; year; month, salinity; temperature. • Climate change threatens fish diversity in Portuguese estuaries due to temperature shifts. [ABSTRACT FROM AUTHOR]