This work aimed to determine the most relevant organic pollutants, especially pesticide residues, in water samples from the protected area of Lake Zobnatica in the Vojvodina region, Serbia. Sampling campaigns were conducted within different seasons related to different agricultural activities in the vicinity of the protected area. The intensive use of pesticides led to the more frequent detection of specific pesticides such as Terbuthylazine, alpha-Cypermethrin, and Aminomethyl phosphonic acid (AMPA) during the summer, compared to the autumn campaign. In addition to these pesticide residues, other organic pollutants, including phthalate esters, fatty acids, phenols, and aldehydes, were also detected. The characterization of water from collectors in the protected area of Lake Zobnatica, in the Vojvodina region, provided reliable data on the contamination of the selected wetland locality required for effective risk assessments and risk management standards of the selected ecosystem. Additionally, three different water pollution indices were calculated using physicochemical data, offering a comprehensive water quality evaluation in the wetland. Environmental risk evaluation identified five compounds with highrisk quotients: diisobutyl phthalate, dibutyl phthalate, eicosane, phenol, 2,4-bis(1,1-dimethylethyl)-, and diphenyl sulfide. Obtained results would enable a more in-depth understanding of wetland problems such as organic pollution and better management of wetland areas to mitigate pollution problems.