In carbon-compound-specific isotope analysis (carbon CSIA) of environmental micropollutants, purification of samples is often required to guarantee accurate measurements of a target compound. A companion paper has brought forward an innovative approach to couple a quartz crystal microbalance (QCM) with high-performance liquid chromatography (HPLC) for the online quantification of matrices during a gradient HPLC purification. This work investigates the benefit for isotope analysis of polar micropollutants typically present in environmental samples. Here, we studied the impact of the natural organic matter (NOM) on the isotopic integrity of model analytes and the suitability of the NOM-to-analyte ratio as a proxy for the sample purity. We further investigated limitations and enhancement of HPLC purification using QCM on C 18 and C 8 phases for single and multiple targets. Strong isotopic shifts of up to 3.3% toward the isotopic signature of NOM were observed for samples with an NOM-to-analyte ratio ≥10. Thanks to QCM, optimization of matrix removal of up to 99.8% of NOM was possible for late-eluting compounds. The efficiency of HPLC purification deteriorated when aiming for simultaneous purification of two or three compounds, leading to up to 2.5% less NOM removal. Our results suggest that one optimized HPLC purification can be achieved through systematic screening of 3 to 5 different gradients, thereby leading to a shift of the boundaries of accurate carbon CSIA by up to 2 orders of magnitude toward lower micropollutant concentrations.