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Marine pollution is a major threat to human and environmental health. Given the complexity of function of marine and coastal ecosystems, it is unlikely that a balanced view of the nature and extent of risk will easily be achieved if human and environmental risk assessments continue to be conducted in isolation. Here, the integration of assessment protocols is advocated as a holistic means of improving risk management. Biomarkers can provide the common conceptual framework and measurable endpoints necessary for successful integration. Examples are given of the ways in which suites of biomarkers encompassing molecular change, cellular pathology and physiological impairment can be developed and adapted for human and ecological scenarios. By placing a greater emphasis on the health status of impacted biota, it is more likely that risk assessment will develop the efficiency, reliability and predictive power to adapt to the unforeseen environmental threats that are an inevitable consequence of human development and global change.