Inter- and intra-estuarine fish assemblage variability patterns along the Portuguese coast

► Inter- and intra-estuarine variability of fish assemblages was studied in nine estuaries. ► River flow was a crucial factor for variation of species richness among estuaries. ► Distinct factors explained changes in species richness within individual estuaries. ► Concerning fish, functional role of an estuary is related with dominant saline area.