Understanding the mechanisms of natural source zone depletion (NSZD) will support an improved understanding of the long-term sustainability of NSZD as a site remedy and how NSZD rates may change over time. This is the first study that has quantified and compared the rate of three NSZD mechanisms (methanogenesis, vaporization, and aqueous biodegradation) between two chemically distinct light non-aqueous phase liquid (LNAPL) source zones (aliphatic-rich naphtha for Zone #1 vs aromatic-rich pyrolysis gasoline for Zone #2) within the same geologic and climate conditions. The rates of NSZD attributable to vaporization (400 mg C/m2/d vs. 300 mg C/m2/d) and aqueous biodegradation (92 mg C/m2/d vs. 67 mg C/m2/d) were similar for Zone #1 and #2; however, the rate of methanogenesis NSZD was 6x higher in Zone #1 (1000 mg C/m2/d vs. 170 mg C/m2/d). These results suggest that the aliphatic hydrocarbons content in an LNAPL source may be a factor in the rate of methanogenesis NSZD. For both Zone #1 and #2, total NSZD rate determined using this “three mechanism” measurement method was in reasonable agreement with two other methods used to measure total NSZD rates (CO2 Gradient Method and Dynamic Closed Chamber Method), validating the “three mechanism” method as a tool to measure the total NSZD rate at a site and to provide an improved understanding of the predominant NSZD mechanism. Overall, this study highlights the importance of LNAPL type and chemical characteristics in determining source zone natural attenuation mechanism and its total rates.