Effective management of contaminated sites requires differentiating and deconvoluting contaminant source impacts in complex environmental systems. The existing source apportionment approaches that use targeted analyses of preselected indicator chemicals are limited whenever target analytes are below the detection limits or derived from multiple sources. However, non-targeted analyses that leverage high-resolution mass spectrometry (HRMS) yield rich datasets that deeply characterize sample-specific chemical compositions, providing additional potential end-members for source differentiation and apportionment. Previous work demonstrated that HRMS fingerprints can define sample uniqueness and support accurate, quantitative source concentration estimates. Here, using two aqueous film-forming foams as representative complex sources, we assessed the qualitative fidelity and quantitative accuracy of HRMS source fingerprints in increasingly complex background matrices. Across all matrices, HRMS-derived source concentration estimates were 0.81 ± 0.11-fold and 0.64 ± 0.24-fold of actual in samples impacted solely by analytical matrix effects (MEs) or by sample processing recovery and analytical MEs, respectively. Isotopic internal standards were not easily paired to individual unidentified non-target features, but bulk internal standard-based abundance corrections improved apportionment accuracy in higher matrix samples (to 0.90 ± 0.12-fold of actual) and/or informed concentration estimate relative errors. HRMS fingerprint mining could identify, based on the dilution behavior, effective individual chemical end-members across 16 homologous series. Although method development is needed, the results further demonstrate the potential applications of non-targeted HRMS data for source apportionment and other quantitative outcomes.