The widespread contamination of sediments has triggered the recognition of the importance that sediments have for the long-term toxicological and ecological properties of aquatic ecosystems. During the past three decades the scientific knowledge on sediment-water exchange processes and the deposition and distribution of pollutants in water and sediment phases has been supplemented by extensive research on the effects of sediment-associated pollutants on aquatic organisms. Basic research in microbiology, ecology and toxicology has uncovered the crucial role of sediment microorganisms for biodegradation of organic matter and cycling of nutrients as well as for the susceptibility of these processes to toxic pollution events. Moreover, microorganisms have found extensive application in aquatic toxicology and various microbial toxicity tests are today available that couple successfully microbial toxicity endpoints to the specificity of the sediment matrix. Sediment-associated toxicants can be brought in contact with test organisms using sediment pore waters, elutriates, extractes or whole-sediment material. Toxicity indication principles for microorganisms are versatile and comprise growth and biomass determinations, respiration or oxygen uptake, bacterial luminescence, the activity of a variety of enzymes and a compendium of genotoxicity assays. The border between toxicological and ecological contaminant effects evaluations in sediments is flexible and long-term ecological predictions should also include an assessment of their pollutant degradation capacities and of key reactions in element cycling. Evaluating microbial community structure and function in environmental systems makes use of modern molecular techniques and bioindicators that could trigger a new quality in the assessment of contaminated sediments in terms of indication of subtoxic effects and early-warning requirements.