Despite its theoretical relationship, the effect of body size on the performance of species distribution models (SDM) has only been assessed in a few studies, and to date, the evidence shows unclear results. In this context, Chilean fishes provide an ideal case to evaluate this relationship due to their short size (fishes between 5 cm and 40 cm) and conservation status, providing evidence for species at the lower end of the worldwide fish size distribution and representing a relevant management tool for species conservation. We assessed the effect of body size on the performance of SDM in nine Chilean river fishes, considering the number of records, performance metrics, and predictor importance. The study was developed in the Bueno and Valdivia basins of southern Chile. We used a neural network modeling algorithm, training models with a cross-validation scheme. The effect of fish size on selected metrics was assessed using linear models and beta regressions. While no relationship between fish size and the number of presences was found, our results indicate that the model specificity increases with fish size. Additionally, the predictive importance of Riparian Vegetation and Within-Channel Structures variables decreases for larger species. Our results suggest that the relationship between the grain of the dataset and the home range of the species could bias SDM, leading in our case, to overprediction of absences. We also suggest that evolutionary adaptation to low slopes among Chilean fishes increases the relevance of riparian vegetation in the SDMs of smaller species. This study provides evidence on how species size may bias SDM, which could potentially be corrected by adjusting the model grain.