Physical habitat simulation (PHABSIM) is an important step of the instream flow incremental methodology (IFIM), which is applied to establish environmental flow regimes. This study applied the PHABSIM in two reaches of the Velhas river basin, whose long-term discharges are similar but are under different degrees of impact. Suitability curves were obtained for fish species using traditional methods (Astyanax sp., Piabarchus stramineus, Piabina argentea and Serrapinnus heterodon) and generalized additive models for fish density (Astyanax sp., P. argentea and S. heterodon). The results of habitat use depended on the method for curves generation. Applying the suitability curves by traditional methods, different discharge scenarios were simulated. The flow increasing from a dry scenario to a discharge of 1 year of return promotes a possible habitat increase for all species. However, the same hydrological flow percentiles produce different habitat proportions in different rivers. This work demonstrates that regardless of how suitability curves for the Neotropical species are generated, caution should be taken when applying them. However, the PHABSIM method allows more complex analyses than the traditional approaches based on minimal flow estimations, which is usually applied in South America.</jats:p>