It is presently well-recognized that the contamination of aquatic sediments in Kosovo is a widespread phenomenon. The observation of the chemical analysis of water and sediments is essential to determine the extent of trace elements in these ecosystems. Hence, in order to be able to determine the mass concentration of the predominant elements present in river Sitnica, inductively coupled plasma mass spectroscopy (ICP-MS) is used for this research. Moreover, a comparison of the mass concentration of water elements with the mass concentration of the elements found in the Sitnica sediments is provided. Utilizing results obtained from ICP-MS analysis, it is shown that the mass concentration of nickel, arsenic, zinc, cadmium, lead, copper, aluminum in certain water sample stations exceeds the permissible sediment quality criteria. Considering the toxicity that heavy metals generate on the aquatic environment, this research aims to assess and measure the metal toxicity, because only then, a proper solution can be suggested to sustain freshwater ecosystems and to prevent constant damage from human activity.