Monitoring fishery resources affected by contaminant discharges can include two distinct components: (1) monitoring contaminant exposure (e.g., residues in fish tissues), and (2) monitoring biological effects. Although exposure monitoring may be appropriate for evaluating the efficacy of ecological restoration programs, effects monitoring is an equally important and often overlooked aspect of monitoring programs. Advantages of monitoring effects indices include (1) biotic integration of diverse exposure pathways and temporal variability; (2) ability to integrate responses across multiple Stressors; and (3) cost effectiveness relative to extensive chemical analyses. The objective of our work was to develop and review biomarker selection criteria including: (1) sensitivity (response time, permanence of response, degree of responsiveness); (2) specificity (specific to contaminant exposure); (3) applicability (cost-effectiveness, scientific acceptance); and (4) reproducibility (biological, methodological). Emphasis is placed on selection criteria for biomarkers associated with organochlorine, petroleum hydrocarbon, or metal exposure and effects.