Hydroelectricity is increasingly used worldwide as a source of renewable energy, and many mountain ranges have dozens or hundreds of hydropower plants, with many more being under construction or planned. Although the ecological impacts of large dams are relatively well known, the effects of small hydropower plants and their weirs have been much less investigated. We studied the effects of water diversion of small hydropower plants on fish assemblages in the upper Ter river basin (Catalonia, NE Spain), which has headwater reaches with good water quality and no large dams but many of such plants. We studied fish populations and habitat features on control and impacted reaches for water diversion of 16 hydropower plants. In the impacted reaches, there was a significantly lower presence of refuges for fish, poorer habitat quality, more pools and less riffles and macrophytes, and shallower water levels. We also observed higher fish abundance, larger mean fish size and better fish condition in the control than in impacted reaches, although the results were species-specific. Accordingly, species composition was also affected, with lower relative abundance of brown trout (Salmo trutta) and Pyrenean minnow (Phoxinus bigerri) in the impacted reaches and higher presence of stone loach (Barbatula quignardi) and Mediterranean barbel (Barbus meridionalis). Our study highlights the effects of water diversion of small hydropower plants from the individual to the population and community levels but probably underestimates them, urging for further assessment and mitigation of these ecological impacts.