Monitoring and control of dangerous substances discharged into receiving waters have attracted more attention lately. Since it is not possible to analyze every single substance, a prioritization methodology is needed for the selection of those to be monitored. Existing well-developed models require significant amount of data for reliable outcomes. This paper presents a methodology to prioritize the dangerous substances having adverse effects on freshwaters in Turkey, where data are scarce. Such a methodology will also serve as a solid model for other countries with limited background data. The adopted methodology enabled the elimination of chemicals to generate a candidate list composed of 608 substances among more than 5000 substances. Further screening and prioritization were conducted using different assessment methods (i.e., Total Hazard Value, Total Impact Value, Combined Monitoring-based, and Modelling-based Priority Setting) to obtain a proposed Final Candidate Specific Pollutants List of 150 dangerous substances. The proposed Candidate National Pollutant List of Turkey was established by combining 45 priority pollutants of the European Union with a list of candidate specific pollutants. According to the outcomes of this study, monitoring and controlling of 195 dangerous substances in freshwaters are recommended. Further detailed studies should be conducted in order to observe the actual levels of these dangerous substances in freshwaters followed by a review of the monitoring list accordingly. Moreover, further revisions might be required in the proposed list due to some possible versatile conditions in terms of sampling points (i.e., change in the location of industries).