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Small hydropower projects (SHPs) are promoted as low‐impact alternatives for large hydropower. SHPs are generally commissioned on small‐ to medium‐sized mountainous rivers, often in biodiverse regions, with backing in the form of subsidies, facultative policies and exemption from impact assessments as they are considered 'green'. However, the ecological impacts of SHPs are understudied especially in highly seasonal tropical streams of Western Ghats of India, a global biodiversity hotspot and a distinct freshwater fish eco‐region. We compared SHP‐affected segments of a dammed and an undammed river in the Western Ghats of Karnataka, to assess how altered flow regime affects seasonal variability in habitat and water quality, and influences fish assemblage structure. We found that flow alteration by the SHP varied between different segments of the dammed river and with season. Furthermore, the nature of flow alteration influenced habitat variability, water quality and fish assemblage response in the dammed river. We observed that the dewatered segment of the dammed river experienced a lotic to lentic shift in habitat and water quality, which favoured fish species with eurytopic affinities. Fluctuating flows in the downstream segment subdued natural variability in flow regime and created novel habitats and water‐quality conditions, affecting fish assemblages. The upstream segment of the dammed river retained natural variability in habitat and water quality, but did not mimic the undammed river in terms of fish composition. We also observed potential constraints on recruitment for migratory species of fish in the dammed river. Based on our results, we suggest how the placement of dewatered segment, and timing the closure of SHP operation in dry season based on ecological thresholds are potential solutions to mitigate the impacts of the SHPs. Furthermore, we recommend effective impact assessments, and adaptive management with active interventions to maintain genetic and ecological connectivity, as key to enhance the sustainability of the SHPs. [ABSTRACT FROM AUTHOR]