Endobenthic species living in close contact with sediment are particularly at risk in contaminated environments. Being relatively sedentary, they cannot avoid deteriorating sediment quality conditions. They are representative of different zoological groups that contribute greatly to ecosystem structure and functioning. Bioaccumulation studies give access to the lability of sediment-bound contaminants, whereas associated risks for biota can be revealed by using biomarkers. Endobenthic invertebrates feed at a low level of the trophic web, but as preys, they have a crucial role in the trophic transfer of contaminants and toxicity. Diverse species exhibit different tolerances to stress, thus providing useful indicators of the health status of communities. For standardized bioassays, numerous species are commercially available, but the use of local species may be more relevant for a precise identification of chemical risk in a local area.