The state of the art of biomarker/bioindicator research in aquatic ecosystems is reviewed. In addition to a theoretical overview, practical examples are given for two biomonitoring attempts (the Trondheim biomonitoring system and the VALIMAR project), which included biomarker/bioindicator applications referring to different levels of biological organization (e.g., physiological biomarkers, histological and ultrastructural diagnoses, or stress protein analyses). In order to answer the question of whether biomarker responses are relevant for effects at higher biological levels (i.e., populations or ecosystems), experimental and theoretical approaches based on the weight of evidence are presented. The suitability of biomarker/bioindicator application to assess environmental pollution in aquatic ecosystems is discussed.