This study analyses the impact of small hydropower plants (HPP) on fish in three Latvian transboundary river basin districts. The MesoHABSIM habitat simulation model was applied to seven Latvian lowland rivers regulated by HPP, four of which belong to the salmonid river type and three to the cyprinid type. Daily stream flow time series for 1961–2018 were used for flow regime calculations in reference (unimpacted) and altered (impacted by HPP operation) flow conditions. Conditional habitat suitability model/criteria for fish were used to assess a potentially available habitat at different flow conditions. Brown trout (Salmo trutta) for salmonid rivers and chub (Squalius cephalus) for cyprinid rivers were selected as case examples to show habitat suitability for different stream types. The authors found significant differences in habitat availability for salmonid and cyprinid rivers, indicating that ecological flows must be calculated separately for fast- and slow-flowing rivers. This study is the first attempt in Latvia to set ecological flow values not only using hydrological calculations but also biological data as an indicator of ecological changes.