Changes in lotic benthic macroinvertebrate assemblages along the transboundary Axios-Vardar River (Greece -Former Yugoslavian Republic of Macedonia) were examined in order to identify major anthropogenic impacts correlated to the benthic community composition during the low flow season. Macrozoobenthos and water samples were collected from 21 sites during summer 2000 and beginning of autumn 2001. Parallel to sampling, the recording of the physical structure of the sites took place using the River Habitat Survey (RHS) method. The multivariate techniques of FUZZY and Canonical Correspondence Analysis (CCA), as well as the Hellenic biotic score (HES) and the habitat quality scores (HMS, HQA) were applied to the data. Total dissolved solids and total suspended solids were found to be the primary factors affecting the structure of the observed communities. Additionally, species composition responded to anthropogenic activities, e. g. untreated sewage effluents, industrial discharges, agricultural runoff, intense water abstraction and impoundment. As expected, macrozoobenthos community composition shifted from sensitive to tolerant taxa where human impacts were most evident.