Water supplies for millions of U.S. individuals exceed maximum contaminant levels for per- and polyfluoroalkyl substances (PFAS). Contemporary and legacy use of aqueous film forming foams (AFFF) is a major contamination source. However, diverse PFAS sources are present within watersheds, making it difficult to isolate their predominant origins. Here we examine PFAS source signatures among six adjacent coastal watersheds on Cape Cod, MA, U.S.A. using multivariate clustering techniques. A distinct signature of AFFF contamination enriched in precursors with six perfluorinated carbons (C6) was identified in watersheds with an AFFF source, while others were enriched in C4 precursors. Principal component analysis of PFAS composition in impacted watersheds showed a decline in precursor composition relative to AFFF stocks and a corresponding increase in terminal perfluoroalkyl sulfonates with < C6 but not those with ≥ C6. Prior work shows that in AFFF stocks, all extractable organofluorine (EOF) can be explained by targeted PFAS and precursors inferred using Bayesian inference on the total oxidizable precursor assay. Using the same techniques for the first time in impacted watersheds, we find that only 24%–63% of the EOF can be explained by targeted PFAS and oxidizable precursors. Our work thus indicates the presence of large non-AFFF organofluorine sources in these coastal watersheds.