The ichthyofauna of the River Minho tidal freshwater wetlands (TFWs) was studied in a semi-enclosed area, between June 2007 and May 2010, to determine temporal patterns of abundance, biomass and species composition. Fish catches, standardized by the number of fyke nets and by the fishing effort, were analysed and related to river flow, water temperature and precipitation. In total, 21 fish species were identified including six non-indigenous species (NIS) which represented 15% of the total captures (yet 43% of the biomass). Regarding ecological guilds, 82% were freshwater species (61% of the biomass) which included all NIS, whereas 13% of the catches were catadromous species (31% biomass) corresponding to eels. Only 4% were estuarine species (1% biomass) and together marine estuarine opportunists and anadromous species accomplished 1% (2 and 6% biomass, respectively). The fish assemblage showed seasonal patterns with a clear distinction between autumn/winter and spring/summer periods. Significant differences in abundance and biomass were also detected between autumn/winter of 2007/2008 and 2008/2009, i.e., inter-annual variations, with the latter period with lower catches yet higher dominance of NIS. Besides, higher water temperature had a significant negative effect on the observed number of species, but a positive effect on the abundance and biomass of NIS. More attention has to be given to TFWs and their role in structuring fish assemblages, because this information is vital for a sound management, conservation and restoration of estuarine areas.