The current challenge to ecotoxicology is to develop tools that allow rapid and cost-efficient detection of those environmental chemicals or their combinations that are responsible for sublethal, chronic toxic effects in exposed organisms. Bioanalytical tools may meet these challenges, particularly if they are mechanism-based. Technically, bioanalytical tools allow rapid and cost-efficient analysis of environmental matrices. Mechanism-based, bioanalytical tools, however, do not only indicate that certain chemicals are there, but-and this is the major advantage of mechanism-based bioanalytical tools (MBBTs)-they indicate that chemicals with a specific mode of toxic action or a specific toxic potential are there. In this way MBBTs bridge exposure and effect assessment and help in a faster identification of the causative agent(s). Several principles of MBBTs, including immunoassays, enzyme inhibition assays, receptor assays and gene induction assays are briefly discussed and their application in processes such as bioassay-directed fractionation is illustrated. The focus of this manuscript is the analytical power of MBBTs in exposure and effect assessment. MBBTs have, however, a much broader potential and can support research on other challenges in ecotoxicology such as mixture effects or multiple effects caused by single pollutants or by various stresses simultaneously.