The dataset contains records of Fishes (Pisces) collected in the River Sabor (NE Portugal) in 2012-2020, in the scope of a study aiming to understand the temporal dynamics of fish communities in relation to natural and anthropogenics drivers in a Mediterranean watershed. The study is part of research carried out at the Long Term Ecological Research Site (LTER) of Baixo Sabor (lter_eu_pt_002; https://deims.org/45722713-80e3-4387-a47b-82c97a6ef62b). The dataset includes data on fish communities obtained through electro-fishing (with restitution) at 74 sampling sites in 2012, and subsequently at 37 of these sites from 2013-2020. Until 2020, the data include a total of 27,514 records of 14 freshwater fish species. Part of these data has already been analised and published (see Ferreira et al., 2016; Mota-Ferreira et al., 2021). The dataset will be regularly updated with additional data from future sampling years.