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Abstract Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical, and physiological markers (i.e., biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation, and ecological effects while enabling a better understanding of the effects of nonchemical stressors. In the case of contaminant stressors, an understanding of chemical modes of toxicity can be incorporated with diagnostic markers of aquatic animal physiology to help understand the health status of aquatic organisms in the field. Furthermore, new approaches in functional genomics and bioinformatics can help discriminate individual chemicals, or groups of chemicals among complex mixtures that may contribute to adverse biological effects. Although the use of biomarkers is not a new paradigm, such approaches have been underused in the context of ecological risk assessment and natural resource damage assessment. From a regulatory standpoint, these approaches can help better assess the complex effects from coastal development activities to assessing ecosystem integrity pre- and post development or site remediation. Integr Environ Assess Manag 2014;10:327–341. © 2014 SETAC Key Points Issues of contaminant bioavailability, bioaccumulation and ecological effects can be clarified by integrating molecular, biochemical and physiological markers (i.e. biomarkers). The health of aquatic ecosystems and species in those systems can be monitored by integrating chemical analysis with carefully selected biomarkers. Although biomarkers are not new, they have not been adopted into ecological risk assessment or natural resource damage assessment.
Hook et al. (Sat,) studied this question.