Paper’s main goal is to establish “RHS reference site”, which will be the basis for future classification of river habitat quality in other regions of Serbia. River habitats in Golijska Moravica and Jerma basin have been assessed and classified by RHS method, and reference values are determined (which would serve for the next research of river habitats in Serbia). In Golijska Moravica and Jerma basin semi–natural and predominantly unmodified habitats with high diversity are dominant. If we compare HQA index of Moravica and Jerma with HQA indexes in some European countries (Austria, Germany) of same river type (small, shallow mountain rivers)we can conclude that sites in Moravica and Jerma basin have higher habitat diversity. Within river basins there are spatial differences of HQA index value. River sites in Moravica and Jerma basin have lower values of HMS index than sites in European countries. The impact of individual characteristics on total HQA and HMS score is also determined in this paper.Results of this paper are important for conservation of natural habitats, for river basin management plans and to estimate environmental impact of future water management activities in these basins.