Abstract. Flow variability determines the conditions of river ecosystem and river ecological functioning. The variability of ecological processes in river ecosystems gradually decreases. Prediction of the environmental flow allowing to keep biological diversity and river health develops as a response to the degradation of aquatic ecosystems overexploited by humen. The goal of the study was to test the influence of river incision on environmental flow estimation based on the macroinvertebrate BMWP_PL index. The 240 macroinvertebrate assemblages of 12 waterbodies varying in the bed substrate, amplitude of discharge were surveyed in southern Poland. The variations in the distribution of 151 466 macroinvertebrates belonging to 92 families were analysed. The similarity of benthic macroinvertebrates reflects the typological division of the rivers into three classes: mountain Tatra streams, mountain flysch rivers, and upland carbonate and silicate rivers (NMDS, ANOSIM, p < 0.001). As a response variable reflecting the macroinvertebrate distribution in the river, environmental parameters, BMWP_PL index was chosen. Our results show that the BMWP_PL index reached its highest values in shallower zones (by the shores) and at high water velocity in the Tatra Rivers or low velocity in most lowland rivers. The river incision significantly increased the values of e-flow calculations in relation to redeposited channels. The area of habitat suitability decreased with the bed incision intensity. In highly incised rivers, the environmental flow values are close to the mean annual flow, suggesting that a high volume of water is needed to obtain good macroinvertebrate conditions. As a consequence, the river downcutting processes and impoverishment of suitable habitats will proceed.