Perchlorate is a known groundwater and drinking water contaminant with natural and manufacturing sources. A trace level ion chromatography tandem mass spectrometry (IC-MS/MS) method has been used to analyze samples from two High Arctic ice caps, where contaminants are exclusively received from atmospheric sources. Depth samples collected from Devon and Agassiz Ice Caps (Nunavut, Canada) demonstrated the seasonal and longer term anthropogenic influence on the atmospheric perchlorate formation. A recently developed method for the analysis of Cr(VI) with a direct isotope dilution (DID) quantification approach demonstrated the capability of the IC-MS/MS instrumentation, complementing the traditional ion chromatography separation with inductively coupled plasma mass spectrometry (ICP-MS) approach presented in method EPA 6800. The technique allowed to compensate for any loss of Cr(VI) occurring between collection and analysis time that can affect sample integrity and introduce possible biases in measured concentrations. The DID method achieved trace level analysis with an MDL of 2 ng/L.