Until recently, parameters from microorganisms were generally not included in risk assessment at a comparable level to animals and plants. However, the major part of global biomass, biodiversity, and ecosystem processes is present in the microbial world and microbiological techniques applicable to risk assessment are becoming available. Two microbial indicators are described based on the usage of multiwell plates with different substrates and a redox indicator for monitoring mineralisation. With both techniques autochthonous microbial communities are analysed. Producing functional fingerprints of the microbial community gives insights into the composition of different functions. This is equivalent to observations of ecological abundance and species composition. When lack of reference sites or reference data renders risk assessment difficult, measurement of the pollution-induced community tolerance (PICT) can provide useful information.