Crude oil contaminated soil cores were collected from a basin that contained oily solids left from three decades of oil production. Hydrocarbon biomarker analyses revealed that the soil extracts were moderately biodegraded compared with the non-degraded source oil. The degree of biodegradation also decreased with core depth (7 cm to 1 m). These data were correlated to compositional changes observed in acidic NSO-compounds that were selectively ionized and mass resolved by negative ion electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). Among the NSO-compounds ionized, the increase in naphthenic acid concentration (e.g., acyclic and alicyclic carboxylic acids) best correlated with the increase in biodegradation (e.g., from non-degraded to moderately degraded) as determined by the hydrocarbon biomarker analyses. The most biodegraded surface extracts (7 cm) exhibited an 80% increase in the abundance of acids relative to the source oil. Use of an internal standard allowed the semi-quantitative determination of the total naphthenic acid concentration, which decreased significantly (P < 0.05) with soil depth. Furthermore, the shift to higher double bond equivalents (DBEs), from acyclic to alicyclic acids, indicated that the increase in acids in the soil extracts was predominantly due to biotic processes. This work demonstrates the potential of ESI FT-ICR MS as a semi-quantitative tool to monitor the production of naphthenic acids during crude oil biotransformation in the environment.