Wastewater treatment systems are a necessity in urban areas and the question is how they impact on natural environmental. The aim of the study was to determine are there geochemical changes present in the sediment upstream and downstream of the discharge site of the treated wastewater of the City of Zagreb. The analysis was performed on samples from 4 sites and the BCR protocol was used for sequential extraction chemical analysis of the sampled sediments. From the results, it can be concluded that most elements (Cu, Zn, Cr, Ni and Pb) have elevated concentrations at the discharge and downstream of the discharge of the sewage treatment plant. Concentrations of the elements of interest in the first step of the BCR protocol (soluble, exchangeable cations, and those related to carbonates) do not exceed the proposed limit values of heavy metals in the sediment and thus do not represent a potential hazard, while observing the total concentrations of all three steps of analysis, Cu, Pb and As elements concentrations (the sum of all three steps of BCR analysis), exceed the limits of the proposed limit values of heavy metals in sediment. The mineral composition of the sediment concur with the lithology of the study area and the lithological characteristics of the area upstream of the study area.