The Rayleigh equation is commonly applied to evaluate the extent of degradation at contaminated sites for which compound-specific isotope analysis (CSIA) data are available. However, it was shown recently that (i) the Rayleigh equation systematically underestimates the extent of biodegradation in physically heterogeneous systems, while (ii) it overestimates biodegradation if sorption-based carbon isotope fractionation is relevant. This paper further explores these two isotope effects not captured by the Rayleigh equation by means of a numerical modeling approach. The reactive multicomponent transport simulations show that the systematic underestimation is considerably larger for fringe-controlled and Monod-type degradation reactions than for previously assumed redox-insensitive first-order degradation kinetics, while for the nonsteady state front portion of plumes, the Rayleigh equation may falsely indicate the occurrence of and/or overestimate biodegradation. The latter anomaly results from carbon isotope fractionation during sorption. It occurs for both supply- controlled degradation at the plume fringe and slow, reaction-controlled degradation inside the plume core. The numerical model approach enables a more accurate interpretation of CSIA data and thereby improves the quantification of biodegradation processes.