In the recent war in Croatia, the karstic area of the country was endangered by hazardous waste, which calls for particular attention because of its exceptional ecological sensitivity. There are strong indications that various organic pollutants have entered the environment. It is also assumed that oil containing polychlorinated biphenyls (PCBs) was spilled in a number of locations. After the penetration in the environment, these substances are quickly absorbed in soil, sediment or bioaccumulated in the organisms of the aquatic ecosystem. In view of the locations of damaged electric transformer stations in Zadar, Bilice and Dubrovnik, there was some speculation on potential hazard posed by organohalogenated toxicants to Lake Vransko and the coastal area around Zadar, Sibenik and Dubrovnik. Samples of sediments and aquatic organisms were collected and analysed, and the results showed no significant or high levels of contaminants in the areas of Lake Vransko, Sibenik, and Dubrovnik (Petka location), while in the Mikulandra Bay near Sibenik, in Rijeka Dubrovacka, Brodanovo location and Marina near the Vruljica Creek in Zadar, significantly higher levels of PCBs were observed and these toxicants were additionally monitored within the APOPSBAL project from 2002 to 2005. The results of these investigations are presented in this paper.