The article aims at assessing the impact of hydraulic characteristics on the habitat quality of mountain and piedmont watercourses. The solution results from the Riverine Habitat Simulation model, where the quality of the aquatic habitat is represented by the weighted usable area (WUA), which is determined using brown trout as the bioindicator. Flow velocity and water depth are basic abiotic characteristics that determine the ratio of suitability of the instream habitat represented by the weighted usable area. The influence of these parameters on the objective evaluation of the habitat quality is the essence of the paper. The measurements were carried out during the summer period at minimum discharges for 17 mountain and piedmont streams in Slovakia. Three methods for assessing the habitat quality were tested, and differences in the results were found to be significant. The evaluation shows the optimum design methods for calculating the weighted usable area.