The River Prut is a transboundary river between Romania and Republic of Moldova. Numerous tributaries from both sides are bringing with their waters also wastewater from treatments plants and runoff from agricultural fields. Among the broad spectrum of pollutants in rivers resulted from human activity most attention is according to organochlorinated compounds. These persistent compounds refer to the group of substances that are not producing naturally into the environment (xenobiotics) and pose a threat to the biosphere. Organochlorinated compounds include organochlorinated pesticides (OCPs) and polychlorinated biphenyls (PCBs) that are similar to pesticides by their physicochemical properties. Residual amounts of chlorinated hydrocarbons fed into rivers mainly due to washout from agricultural fields and large-scale atmospheric transport. Bottom sediments are an important component of water ecosystems, where most of the organic and inorganic substances are accumulating, including the most dangerous and toxic. Under certain conditions leading to a change hydrodynamic situation, composition and properties of water and other factors, they can become a source of secondary water pollution. In this study, sediments samples were collected in summer 2016 from the Prut River to evaluate the contamination and ecological risks caused by several POPs. Sampling points were selected along the Moldovan side. Automated Soxhlet extraction technique was used for samples processing. The extracts were concentrated and treated with activated copper to remove the sulfur-containig substances, followed by cleaning up on silica gel column. The final solution was further concentrated up to 300 μL and analyzed using gas chromatography coupled to mass-spectrometry (GC-MS/MS). Strict quality assurance and controls were implemented throughout the whole analysis process. For every batch of 4 samples one solvent blank was run to check for interference and cross-contamination. Prior to extraction, each sample was spiked with internal standard (mix of DDX, PCBs) and recovery standard was added prior to injection in GC.