To obtain a more detailed picture of the water quality changes in river longitudinal profiles, an original biological monitoring system has been developed by the Water Research Institute (WRI) in Brno. The system is based on the exact selection of representative macrozoobenthic sampling points. A precise taxonomic identification and statistical evaluation create the basis for documentation of the present water quality and consequently for a water quality simulation model. The biological monitoring system enables information from basic chemical monitoring to be enhanced, and constitutes an eco-engineering tool for the central and regional control of the water quality. A potential cost reduction, when compared to classical modelling techniques, is a benefit which cannot be ignored. The system described is applied in the watershed of the river Morava as given in this paper, as well as for the whole Czech Republic.