Water diversion for hydropower plants is one of the leading causes of habitat alteration and biotic homogenization. The impacts of small hydropower plants on fish communities are usually assessed using taxonomic composition and structure indicators. Size-based indicators are useful tools to evaluate the effects of environmental factors and anthropogenic perturbations on riverine ecosystems. In this study, we investigated the impact of water diversion on fish community body size structure in 16 small hydropower plants in the upper Ter River basin (NE Iberian Peninsula). We tested the use of multiple size-based metrics under different sampling intensities (one- vs. four-pass electrofishing) and compared control vs. diverted stream stretches. Results revealed that water diversion had a negative effect on fish community average and median length, while size spectrum and size diversity metrics showed no responses to the impact. Altitude was positively related with body size metrics and was the strongest natural driver affecting them. Moreover, we found that all the size-based metrics exhibited consistent values under different sampling efforts. Our findings suggest that size-based metrics could be useful indicators for bioassessment of river flow alteration and that one-pass electrofishing was robust enough to characterize the stream fish community size structure in our study.