The potential for the use of biochemical and genetic methods in toxicological risk assessment and in developing bioremediation strategies is expanding rapidly as new methodologies become available. In this paper we present an overview of some of the methods we feel have the most potential for use in assessment and monitoring in the field. Molecular based biosensors and biomarkers can function as measurable indicators of cellular or biochemical responses to stress. They can function not only in the detection of toxic compounds, but can predict their potential risks from a biological and ecological perspective and can thus, be used as early warning systems of the risks associated with specific pollutions. Other biochemical and genetic techniques allow us to detect specific microorganisms and their activities in environmental systems. With these methods the potential biological activity of a contaminated site can be assessed and followed during clean-up. Specific examples from our laboratory demonstrating the use of PCR, in situ hybridization and specific antibodies in environmental microbiology are given. We have also raised a number of questions that still must be answered in order to gain the most from the use of biological tools in environmental monitoring and remediation assessment.