This study outlines the development and subsequent validation of a method using chelation ion chromatography (CIC) pretreatment followed by traditional ion chromatography (IC) and post column UV/vis detection to measure transition metals in fossil fuel wastewaters, such as oil & gas (O&G) brines and coal mine drainage (CMD) waters. Measurement of transition metals is often an important characterization step in the research of environmental and energy systems. IC represents one way to measure these metals with the advantages of being versatile, simple and relatively low cost compared to other analytical methods. However, high concentrations of alkali and alkaline earth metals present in fossil fuel wastewaters will decrease IC detectability of transition metals in these waters. In this study, a CIC method was developed for the analysis of transition metal ions (Fe3+, Cu2+, Ni2+, Zn2+, Co2+, Mn2+, and Fe2+) in fossil fuel associated wastewaters such as Appalachian CMD and O&G wastewaters from the Permian and Bakken shale basins in the United States. CIC system incorporated an on-line chelator column (e.g., the MetPac CC-1) with high selectivity for transition metals over alkali and alkaline earth metals for salt matrix removal prior to transition metal separation and detection. Additional method developments also included acidifying all samples to 2% v/v HCl and using gradient elution rather than isocratic. The recoverability of transition metals in simple salt solutions commonly found in CMD and brine samples (e.g. NaCl, Na2SO4, CaCl2) using CIC was evaluated and compared to that using traditional IC. Our results found that the CIC system significantly improved transition metal recoveries for samples in 10,000 mg/L CaCl2 matrix, reaching 87%-108% recovery for all analytes, as opposed to 2–323% recovery in traditional IC. The limits of detection in this study achieved 10.09–161.2 μg/L, comparable to reported values in similar IC studies. The developed method was also verified with certified water samples, resulting in 89%–111% recoveries in samples with higher analyte concentrations (i.e. >4x the LoDs). The developed method achieved 87%–112% recoveries for most analytes in CMD samples and 72%–138% recoveries for Bakken shale samples, relative to ICP-MS values. Overall, the current IC method can be a very good screening tool for fast and cheap analysis for transition metals at mg/L level, to facilitate selection of samples for more detailed ICP-MS analysis.