The meso-scale habitat simulation model MesoHABSIM was applied in three Lithuanian lowland rivers to study the effect of low-head hydropower plants (HPPs) on the fish habitats. Stream flow time series on a daily scale for the period 1970-2015 were used to describe flow regime downstream of HPPs for periods before and after their installation. Conditional habitat suitability criteria were developed for 4 species of cyprinid fish, schneider (Alburnoides bipunctatus), dace (Leuciscus leuciscus), roach (Rutilus rutilus) and vimba (Vimba vimba) to simulate their available habitat at different water discharges. Modelling results showed that HPPs have a significant impact on habitat availability in the low flow period in dry years below HPPs due to insufficient released flow. The environmental flow, as prescribed by the Lithuanian national law, is estimated between 80 and 95% exceedance probability of the mean minimum discharge of 30 days. This flow leads to a significant reduction in frequency and duration of available suitable habitats for vimba and schneider during low flow period. The roach habitat is the least affected. The results of habitat modelling are in line with the actual data on the occurrence and relative abundance of considered fish species in the studied river stretches. A general comparison of the relative abundance of modelled fish species in 42 natural river stretches and 20 stretches below the HPPs also showed that the relative abundance of roach is significantly higher, and that of schneider is significantly lower in river sections below the HPPs than the abundance in natural river sections. All results indicate that the current environmental flow does not secure survival of certain fish species. The applicability of the average low flow release during summer could be a plausible alternative to the current environmental flow in order to maintain ecosystem health and services.