A pilot study is presented evaluating selected chlorinated pesticides as chemical tracers for water masses in a sub-Arctic fjord system (Godthåbsfjord, western Greenland). Polyoxymethylene (POM) based passive water samplers were deployed during summer–autumn 2010. The levels of the analysed chlorinated pesticides in the fjord surface waters were found to be low compared to earlier studies. α-Hexachlorocyclohexane (α-HCH) and hexachlorobenzene (HCB) were the predominant contaminants. However, these two compounds have higher levels in oceanic water compared to freshwater influenced fjord waters. These chemicals can thus be considered as indicators for direct atmospheric long-range transport, while the organochlorine pesticides like trans-, cis-chlordane, trans-nonachlor and oxychlordane that are detected in the inner parts of the fjord are indicators for potential freshwater sources such as rivers and glacial meltwater runoff (secondary sources). The average values were 50 pg L⁻¹ for HCB and 11 pg L⁻¹ for α-HCH. These concentrations are comparable to levels in fjords in Svalbard (Norwegian Arctic), but lower than in open and/or ice covered oceans in the Canadian Arctic. Two air samplers were deployed for the identification of direct atmospheric contributions. Local contamination sources do not contribute significantly. The study demonstrated the value of passive water sampling devices for comprehensive hydrological characterization of Arctic coastal waters.