Body size data of stream fish in the north-east of the Iberian Peninsula. We provide a unique fish individual body size dataset collected from our own sampling and public sources in north-eastern Spain. The dataset includes individual body size measures (fork length and mass) of 12,288 individuals of 24 fish species within 10 families collected at 118 locations in large rivers and small streams. Fish were caught by one-pass electrofishing following European standard protocols. The fish dataset has information on the local instream conditions including climatic variables (i.e., temperature and precipitation), topography (i.e., altitude), nutrient concentration (i.e., total phosphorus and nitrates), and the IMPRESS values (a measure of cumulative human impacts in lotic ecosystems). The potential uses of this new fish dataset are manifold, including developing size-based indices to further estimate the ecological status of freshwater ecosystems, allometric models, and analysis of variation in body size structure along environmental gradients.