Naphthenic acid fraction compounds (NAFCs) are a toxicologically relevant component of oil sands process-affected materials (OSPM). For the first time, we report on differences in the concentrations and distribution of NAFCs from wetlands on an Athabasca oil sands mine site with varied histories of solid and liquid OSPM input. Sampling locations included natural and naturalized reference wetlands, a reclaimed tailings pond, wetlands supplemented with OSPM, opportunistic wetlands, and tailings ponds. Samples were prepared using solid-phase extraction, and analyzed by high-resolution Orbitrap mass spectrometry; NAFC concentrations and characteristics were evaluated for all locations. The NAFCs from tailings ponds were dominated by O3-NAFCs and classical naphthenic acids (NAs; i.e., O2 species) with double bond equivalences of 3 and 4. Reference wetlands had no dominant species, and relatively little NAFC content. The heteroatomic species in opportunistic wetlands were dominated by highly-oxidized NAFC species, where Σ [O3:O6] species constituted 55–75% of the assignable spectrum and 3–4% NAs; in tailings ponds NAs constituted 47–51%. A relatively young (4-year-old) wetland built on a former tailings pond had NAFC concentrations between 65 and 80 mg/L, and NAs constituted 47% of the assignable spectrum. There was thus little apparent oxidation of NAFCs at this young wetland. The composition of NAFCs from one wetland (≥15 years old) supplemented with OSPM contained a greater proportion of oxidized species than tailings, suggesting NAFC transformation therein. These data suggest that while NAFCs are persistent in some wetlands, there is preliminary evidence for oxidation in mature wetlands.