Abstract. This work represents an attempt to define a simple method to classify the relative degree of disturbance of sites in lotic systems on the basis of comparison of their faunistic composition with reference sites. Two ecotypes were selected in northern Portugal where benthic invertebrates were sampled in reaches with different levels of contamination. As a first stage, previous Geographic Information System information was used to define reference sites in each ecotype. Afterwards, multivariate techniques and non linear estimation models were combined to assess biological quality. This method allowed us to quantify sites according to increasing levels of contamination, after the probabilities of occurrence of taxa along a gradient of contamination taking into account the reference condition. The results suggest that this method is sensitive to organic pollution, easy to interpret, namely the species tolerance, and could be a good framework to establish regional rankings depending on the ecological impact of river sites.