An overview of the tasks accomplished in the frame of the research project is given. The motive for the study is lack of available tools and methodology that would enable objective evaluation of fish habitat suitability of an examined river section, taking into account the quantities of water allocations and executed mitigation measures, respectively. Methodology will be based on the calculated hydraulic parameters (discharge, flow velocities, and water depth) and other hydromorphologic stream parameters (substratum, fish covers) for different discharges. The main objective of the project is implementing up-to-date information tools and methods that will allow more accurate definition of environmentally acceptable flow, considering also the assessment of the mitigation measures efficiency. Aforementioned will also be a basis for enabling an integral assessment of groundwork for adoption of measures to preserve and restore fishery resources. The paper presents the theoretical background and information tool based on the fuzzy logic approach and the needed data input, such as collecting data and analyses that need to be accomplished before starting habitat modelling. To illuminate the establishment of the models and the course of analyses the paper also shows the preliminary results of fish sampling on Radovna River. Paper conclusion unveils the essential findings so far made and the problems that should be taken in to account to perform efficient habitat modelling.