The article is focused on the process of evaluation of the quality of aquatic habitats. The habitat quality is characterized by bioindication, which is represented by ichtyofauna in habitat suitability curves. During the periods of minimum flows the ichtyofauna prefers covers with deeper habitats. This has been showed by the correlation of suitability curve characteristics for water depth. The curves are based on the frequency sorting of the fish in microhabitat, which were determined on the basis of the ichtyological survey. Accuracy assessment of the suitability curves is one of the most important steps in the IFIM methodology. Evaluation and generalization of the suitability curves for Schneider (Alburnoides bipunctatus) was done in the Nitrica River. The suitability curves were processed for two abiotic parameters – depth and velocity. Hydraulic and ichthyologic measurements were performed in summer 2013. The morphology of the Nitrica River was measured for needs of 2D hydraulic modeling, which was performed by 2D model DHI MIKE 21FM. The results of weighted usable area show that the Schneider prefers minimum range of flows.