In this study we present and apply a methodology for identifying environmentally hazardous compounds in food industry wastewaters (FIW). The methodology comprises a source analysis and a hazard screening of xenobiotic organic compounds based on environmental distribution, persistence, bioaccumulation, and toxicity in aqueous and solid phases. This approach was applied to four selected FIW representing fish, pork meat, and vegetable production. Included in this approach was an analytical–chemical screening of 137 xenobiotic organic compounds showing that 13 compounds and groups of compounds could be detected in the FIW composite samples. The combined source analysis revealed that 161 xenobiotic organic compounds could potentially be present in these four FIW. The main sources were raw materials and their processing, but also packaging and cleaning of the production facility contributed to the total number of compounds potentially present. Using the hazard screening procedure it was found that 29 and 102 compounds should be considered for further hazard assessment in the aqueous and solid phases, respectively. It is important to note that 12% of the 161 compounds could not be evaluated for environmental hazards due to lack of inherent data on degradability, toxicity, and bioaccumulation. Furthermore, for 91% of the compounds no information was found on anaerobic biodegradability. The presented procedure contributes with a systematic source analysis and a ranking of the xenobiotic organic compounds that could cause environmental concern. In this way the procedure can provide guidance to operators and decision makers on handling options for wastewater streams in food processing industries.