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Legacy perfluorinated compounds exhibit significant environmental persistence and bioaccumulation potential, which has spawned an ongoing effort to introduce replacement compounds with reduced toxicological risk profiles. Many of these emerging chemical species lack validated quantitative methods, and, frequently, appropriate analytical standards for accurate monitoring and identification. To fill this knowledge gap, a general method for the quantitative determination of perfluoroether carboxylic acids (PFECAs) by LC-MS/MS was single-lab validated on spike-recovery samples in surface, drinking, and wastewater for a variety of perfluorinated ether standards. Relative error measurements for spike-recovery samples in each matrix ranged from 0.36% to 25.9%, with an average error of 10% overall. Coefficient of variation (CV) for each compound ranged from 10 to 28% with an average of 17%. The quantitative methodology was applied during repeated weekly monitoring of the Cape Fear River during remediation of PFECA hexafluoropropyloxide dimer-acid (HFPO-DA), known by the brand name "GenX." Semi-quantitative concentration estimates for emerging PFECA compounds lacking analytical standards was also carried out using surrogate calibration curves and mass labeled HFPO-DA as an internal standard. Estimates of the emerging compounds were possible using matched standards, but application of the estimation methodology to compounds with known concentration revealed that such estimates may possess up to an order of magnitude, or more, in uncertainty due to the difficulty of matching with an appropriate standard. Nevertheless, the estimation biases are primarily systematic (extraction efficiency and instrument response) rather than stochastic, enabling the collection of time-course data; both HFPO-DA and the emerging compounds were reduced in surface water and drinking water concentration of several orders of magnitude after removal of the source waste stream. Published by Elsevier B.V.