Due to an incomplete elimination in wastewater treatment plant (WWTP), the residues of contaminants are found both in waste and surface waters. Many of these compounds provide a means of identification sources of inputs and pathways of movement of chemicals through ecosystem. In respect to this, one of priority tasks is to determine the environmental distribution of organic pollutants in the surface waters. Both anthropogenic and naturally occurring compounds are found mixed together in recent environmental samples and several of these compounds may be used as tracers to study natural processes affecting the fate and effects of chemical contaminants in water. In the south-eastern of Europe there is little information on river water status [1]. The existent data refers at some metal trace in very critical sites, general quality studies by analyzing the benthic macrofauna but information on anthropogenic organic pollutants as individual compounds is limited to only few emerging contaminants [2]. Therefore a systematic structural investigation of individual molecular pollutant present in environmental water at regional level is important. The present paper purpose is the characterization of organic pollutants to evaluate the degree of contamination of the river waters in high populated catchments from South-Eastern of Europe. The samples were collected from few places along of the Prut River, Border River between Romania and the Republic of Moldova. The samples were collected by three techniques: a) grab sample, b) using composite sample devices and c) by passive samples devices. The analyses were performed using a GC/MS system. The families of pollutants was visualised by chromatograms on diagnostic ions [3]. A systematic study of individual compound as structure and quantity in region of the border Romania- the Republic of Moldova was done based on experimental data on a big number of samples. The molecular marker compounds will be used in the subsequent monitoring activities to obtain the complete image of the specific pollutants in the Prut Basin in different seasons. A number of 67 of compounds were identified. The quantity of pollutants was calculated using isotopic labeled compounds. The structure and quantity of detected compounds are discussed in relation to collection places and seasons.