The main goal of this work was to suggest to authorities concerned a monitoring network on main rivers of Kosovo. We aim to suggest application of WFD (Water Framework Directive) in Kosovo as soon as possible. Our present chemical research could be the first step towards it, giving an opportunity to plan the monitoring network in which pollution locations will be highlighted. In addition to chemical, future ecological studies could be performed. Waters of the rivers Drini i Bardhë, Morava e Binçës, Lepenc and Sitnica, which are of supra-regional interest, are investigated systematically along the river course. Sediments of these rivers were also investigated at the same monitoring points and results have recently been published by us. In this paper we present results of mass concentrations of eco-toxic metals: Cu(II), Pb(II), Cd(II), Zn(II) and Mn(II) in waters of four main rivers of Kosovo, using Anodic Stripping Voltammetry (ASV), Atomic Absorption Spectrophotometry (AAS) and Ultraviolet-Visible (UV-VIS) Spectrometry. Also some physico-chemical parameters are determined: water temperature, electrical conductivity, pH, alkalinity, total hardness and temporary hardness. Results of concentrations of eco-toxic metals in water are compared with concentrations found in sediments at the same locations. Statistical methods are applied to determine anomalous regions Classification of waters at each sampling station of our work was tentatively performed based on metal indicators, using Croatian standards. Our results are showing that concentrations of Zn in all waters are low and pose no risk for living organisms. Exception is water at S5 station, where concentration is above permanent toxic level. Concentrations of Pb and Mn are high at D5 station on Drini i Bardhë River (14 km from boarder to Albania) and at all stations along Sitnica River. Cadmium in high concentrations which is above permanent toxic level is measured in water only at two stations, one (M1) on Morava e Binçës River and the other (S5) on Sitnica River (56 km from boarder to Serbia). Comparison with available results from the past shows that water pollution with respect to toxic elements decreased since 1989, what is explained with closing of heavy industry since then. Continuation of water and sediment monitoring using more than one experimental technique is highly recommended, particularly at locations S2 and S5 with anomalous concentrations of toxic elements, as well as establishing of permanent network of monitoring stations by Kosovo authorities. Remediation of sediments at polluted locations in Sitnica River would be desirable.