The microbial community dynamics inside biogeochemical reactors is a key issue to both successful treatment and longevity of performance. Typically, the reactors are operated to promote sulfate-reducing bacteria (SRB) in order to generate the biogenic metal precipitating reagent sulfide. However, SRB are dependent on the activities of other microbes such as cellulose degraders and fermenters to obtain the requisite organic substrates. This presentation will review recent efforts to identify the main microbiological species, quantify active microbial function and track organic substrate consumption in a number of different biogeochemical reactors.