This paper reviews the present state of municipal wastewater treatment in the Slovak Republic. A comprehensive approach was applied to the problem; particular elements of water quality control systems were studied and subsequently their interactions were considered. Analysis of available data in this field shows the serious problems concerned with the performance and maintenance of existing sewer systems and wastewater treatment plants as well as with their process efficiency and impact on the water quality of receivers. The significant influence of groundwater infiltration and industrial wastewaters on municipal wastewater quality and their impact on effluent quality are documented. All these facts were evaluated and priorities were set for improving the water quality control and the utilization of integrated urban water quality management, keeping in mind the typical socio-economic problems encountered during the transition of post-communist countries.