Mathematical modelling should be regarded as just another tool by microbial ecologists. Unfortunately, they seem to shun mathematical modelling approaches to biological systems. This text, a collaboration between mathematicians and microbial ecologists, attempts to change the state of affairs. It presents approximately a dozen specific applications of mathematical modelling in microbial ecology. Among the areas touched upon are biofilms, biodegradation, bioreactors, the microbes of the gut and rumen, soil systems and nitrogen transformation, and estuarine and benthic systems.