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The growth in readily available computational resources has led to increasingly sophisticated numerical models of biologically mediated, reactive chemical transport in aquifers. Such models are able to both simulate and predict behaviour of contaminants over reasonably long time scales and under a variety of circumstances and conditions. Application of one such model is demonstrated in two contamination scenarios, each of which constitutes a significant environmental problem. The first concerns acid mine drainage (AMD), a widespread problem facing mining and other industries. The second concerns contamination of soil and groundwater by benzene, toluene, ethylbenzene, xylene (BTEX) compounds, resulting from spills or leaks of petroleum hydrocarbons. In each case, the model is used to simulate both the production and evolution of the contaminants as they migrate in groundwater, and also to evaluate remediation schemes.