Deterioration of water quality is a major problem world widely according to many international non-governmental organizations (NGO). As one of the European Union (EU) countries, Bulgaria is also obliged by EU legislation to maintain best practices in assessing surface water quality and the efficiency of wastewater treatment processes. For these reasons studies were undertaken to utilize ecotoxicological (Microtox®, Phytotoxkit FTM, Daphtoxkit FTM), instrumental (to determine pH, electrical conductivity (EC), chemical oxygen demand, total suspended solids (TSS), total nitrogen (N) and phosphorus (P), chlorides, sulphates, Cr, Co, Cu, Cd, Ba, V, Mn, Fe, Ni, Zn, Se, Pb), as well as advanced chemometric methods (partial least squares–discriminant analysis (PLS-DA)) in data evaluation to comprehensively assess wastewater treatment plants' (WWTPs) effluents and surface waters quality around 21 major Bulgarian cities. The PLS-DA classification model for the physicochemical parameters gave excellent discrimination between WWTP effluents and surface waters with 93.65% correct predictions (with significant contribution of EC, TSS, P, N, Cl, Fe, Zn, and Se). The classification model based on ecotoxicological data identifies the plant test endpoints as having a greater impact on the classification model efficiency than bacterial, or crustaceans’ endpoints studied.