Sediment dredging is necessary to sustain navigation infrastructure in ports and harbor areas. In the United States alone between 250 and 300 million cubic yards of sediment are dredged annually. Dredging activities may cause stress on aquatic biota by locally increasing turbidity and suspended sediment concentrations, physically disturbing habitat by elevated sedimentation rates, interfering in migratory behaviors, and hydraulically entraining bottom dwelling organisms. Environmental windows are a management practice used to alleviate such stresses on resident and transient biota by placing temporal restrictions on the conduct of dredging operations. Adherence to environmental windows can significantly inflate costs for project sponsors and local stakeholders. Since their inception following passage of NEPA in 1969 the process for setting environmental windows has not followed structured procedures and represents an example of the difficulty inherent in achieving a balance between biological resource protection and cost-effective construction and maintenance of navigation infrastructure. Recent developments in the fields of risk assessment for non-chemical stressors as well as experience in implementing structured risk-informed decision-making tools for sediment and natural resource management are summarized in this paper in relation to setting environmental windows. Combining risk assessment and multi-criteria decision analysis allows development of a framework for an objective process consistent with recommendations by the National Academy of Sciences for setting environmental windows. A hypothetical application of the framework for protection of Pacific herring (Clupea pallasii) in San Francisco Bay is discussed.