The article focuses on adapting generalized depth preference and flow velocity characteristics from Brown trout (Salmo trutta morpha fario) to the Minnow (Phoxinus phoxinus). The results obtained were used to model habitat suitability with 1D and 2D models. Since 1995, research on assessing aquatic habitat quality has been ongoing on 77 mountain streams in Slovakia. This assessment employs a System of Environmental Flow Analysis (SEFA), which is based on the Instream Flow Incremental Methodology (IFIM). In most sections, Brown trout occurred in representative numbers. Brown trout habitat preferences were derived and generalized, and represented by suitability curves. Minnows were present in sufficient numbers for the derivation of suitability curves only on some streams, making direct generalization from the measured data unrepresentative. The measurement results showed that Minnow has similar depth and flow rate preferences to Brown trout. Therefore, it can be assumed that it is possible to adapt the generalised suitability curves from Brown trout to Minnow. This expansion enabled us to broaden the assessment of habitat quality using the SEFA model to mountain streams that are dominated by Minnows and where there is insufficient Brown trout presence. Verification of parameter adaptation from Brown trout to Minnow was conducted in 11 sections of mountain streams. We discuss the performance of habitat quality modeling, concerning the fundamental hydraulic characteristics of streams, using both 1D and 2D models. The results of the 2D modeling are presented for a sub-mountain stream.