Hydropower development is rapidly expanding in biodiversity-rich regions like the Ecuadorian Andes, raising major concerns about its ecological impacts. This study evaluates fish species composition and habitat characteristics in the Cristal and Dulcepamba Rivers, with a particular focus on the effects of the San José del Tambo Hydroelectric Project on the Dulcepamba River. Sampling conducted during the dry season (November–December 2023) at 15 sites incorporated fish surveys, habitat analyses, and environmental quality evaluation. The results showed marked declines in fish abundance, richness, and diversity in sections of the Dulcepamba River directly affected by water diversions, with species richness reduced to only three species at a site most impacted by discharge reduction. Conversely, the Cristal River, with its unaltered hydrology, supported considerably greater diversity, including 12 species at one site. Environmental integrity indices (Andean–Amazon Biotic Index, Biological Monitoring Working Party Index, Andean Riparian Quality Index, and Fluvial Habitat Index) further underscored the Cristal River’s superior conservation status. In the Dulcepamba River, reduced discharge in the environmental flow of the Hydroelectric Project—below mandated environmental discharge levels—led to river drying, disrupted connectivity, and impaired fish migration. This study provides essential insights into these highly biodiverse yet poorly studied ecosystems, which are increasingly threatened by anthropogenic pressures. The findings highlight the critical need to reconcile energy development with conservation efforts in these vulnerable Andean environments.
