Substrate removal rates of biofilms, which occur at sediment-water interfaces and on other submerged aquatic surfaces, depend on whether the rates are predominantly limited by diffusion rates of the substrate to and into the biofilms or by the kinetics of microorganisms that remove the substrate from solution. A reasonable understanding of the interrelationship of these processes requires a knowledge of how diffusion limitation affects species diversity and, therefore, the ultimate kinetic limitations of biofilms to transform a substrate. Mathematical models designed to predict substrate removal rates under field conditions must incorporate a capability to predict whether diffusion or microbial kinetics will dominate substrate removal rates for a particular substrate under a particular set of environmental conditions. A possible solution to this modeling problem involves the use of subroutines to estimate diffusion rates to compare with microbial transformation rates based on laboratory-determined rate coefficients for kinetically limited substrate removal rates of blended biofilm samples.