Understanding the dynamics of sorption and bioavailability is crucial to the success of transport models as bioavailability often limits the complete bioremediation of contaminated soils. This paper examines the interplay between sorption and bioavailability with pulsed injection of nutrients based on a mechanistic model of microbially mediated reactive transport. We used a dimensionless parametric approach based on nondimensional groups such as the Damk¿hler and Peclet numbers to assess the relative importance of processes and rates. We consider case studies involving the biodegradation of carbon tetrachloride (CT) as well as a chemically induced degradation system to evaluate the effects of bioavailability. We first used these two cases to explore the effects of selectively activating the degradation terms in the aqueous and sorbed phases. The models for these two cases consistently predict that degradation is insensitive to retardation if degradation terms are not included for the sorbed phase. A specific mass removal rate was developed as an efficiency metric to explore the effects of pulsed nutrient injection on contaminant degradation and to estimate an optimal injection interval. The contaminant mass degraded per unit pumping was shown to be significantly higher for pulsed injection of substrates than with continuous injection. The presented results clearly indicate that considerations of bioavailability profoundly alter model predictions of degradation as well as parameter estimation results.