Considering human population growth and the increasing demands for safe drinking water, there is a need to manage groundwater resources effectively. This text explores the microbial characterization of aquifers, supplying information on hydrogeology and groundwater contamination. It focuses mainly on: sampling methodologies; detection of bacterial, protozan, viral and other microbial pathogens; microbial modelling and transport; DNA fingerprinting and other microbial characterization approaches; and microbial risk assessment groundwater applications.