Microbial processes are now perceived to be an important component of the marine food chain. Mathematical models present a quantitative means of analysing interspecies interactions within food webs. Although detailed models of individual components of the microbial food web (bacteria, phytoplankton, protozoan predators) have been derived, their incorporation into large-scale food web models has yet to become commonplace. Current models have confirmed the general importance of microbial food webs and that the specific inclusion of protozoan predators in models is often necessary to simulate the observed dynamics. Simulations have indicated that the effect of the microbial food web on the food chain may vary greatly depending on imposed physical or biological conditions. The manner in which nutrient regeneration from protozoan predators and its subsequent reutilisation by bacteria and phytoplankton is simulated is an important consideration. Models employ equations of varying sophistication, but detailed recent formulations use a dual model currency of C and N. Models have also increased our understanding of the interaction between grazing and nutrient cycling and the different behaviour of food chains and webs.