Environmental biotechnology is evolving. Current process objectives include the production of chemicals and/or energy carriers (biofuels) in addition to the traditional objective of removing pollutants from waste. To maximise product yields and minimise biomass production, future processes will rely on anaerobic microbial communities. Anaerobic processes are characterised by small Gibbs energy changes in the reactions catalysed, and this provides clear thermodynamic process boundaries. Here, a Gibbs-energy-based methodology is proposed for mathematical modelling of energy-limited anaerobic ecosystems. This methodology provides a basis for the description of microbial activities as a function of environmental factors, which will allow enhanced catalysis of specific reactions of interest for process development.