The environmental pollutions generated by human activities are important concerns that environmental risk assessment procedures have the purpose to evaluate and mitigate the effects. Microorganisms are among the first impacted by human generated pollutions. Furthermore, because they are essential actors in ecosystem functioning the evaluation of the pollution effects on microorganisms is of paramount importance. Their response may serve as proxy to report the effects on, and the recovering capacities of, the ecosystem. The behaviour of microorganisms in response to chemical pollution has been largely studied. In this chapter, we introduce the mechanisms underlying the microbial adaptation capacities involved in response to pollutants. We also discuss the basic knowledge inspiring microbial ecotoxicological tools reporting the pollutant effects that have been developed at the different biological organization levels, from genes and cellular processes to population and microbial community responses.