Stable isotope data have been increasingly used to assess in situ biodegradation of organic contaminants in groundwater. The data are usually evaluated using the Rayleigh equation to evaluate whether isotope data follow a Rayleigh trend, to calculate the extent of contaminant biodegradation, or to estimate first-order rate constants. However, the Rayleigh equation was developed for homogeneous systems while in the subsurface, contaminants can migrate at different velocities due to physical heterogeneity. This paper presents a method to quantify the systematic effect that is introduced by applying the Rayleigh equation to field isotope data. For this purpose, the travel time distribution between source and sampling point is characterized by an analytical solution to the advection-dispersion equation. The systematic effect was evaluated as a function of the magnitude of physical heterogeneity, geometry of the contaminant plume, and degree of biodegradation. Results revealed that the systematic effect always leads to an underestimation of the actual values of isotope enrichment factors, the extent of biodegradation, or first-order rate constants, especially in the dispersion-dominant region representing a higher degree of physical heterogeneity. A substantial systematic effect occurs especially for the quantification of first-order rate constants (up to 50% underestimation of actual rate) while it is relatively small for quantification of the extent of biodegradation (< 5% underestimation of actual degree of biodegradation). The magnitude of the systematic effect is in the same range as the uncertainty due to uncertainty of the analytical data, of the isotope enrichment factor, and the average travel time.