Implementing marine ecosystem-based management at regional and small spatial scales is challenging due to the complexity of ecosystems, human activities, their interactions and multilayered governance. Ecological risk assessments (ERAs) of marine biodiversity are often used to prioirtise issues but only give broad guidance of how issues might be addressed in the form of strategies. However, at small and regional spatial scales marine natural resource managers have to make decisions within these strategies about how to manage specific interactions between human uses and ecological components. By using the transition between risk characterization and risk treatment in ERA for marine biodiversity tractable ways through the complexity can be found. This paper will argue that specific management and research actions relevant to smaller spatial scales can be developed by using the linkage between risk factors and risk treatment in ERA. Many risk factors require risk treatments that extend beyond the boundary of local agencies or sector responsibilities. The risk factor-treatment platform provides a practical way that these boundaries can be opened up by providing a scientifically based and transparent process to engage all actors who need to be involved in addressing the issues raised by an ERA. First, the principles of the mechanism will be described. Second, how the mechanism is constructed will be introduced using examples from an urban estuary. Application of the mechanism reveals three different types of risk factors (stressor, ecological, and knowledge gap) that can be used to develop specific management and research actions to treat risks. The systematic approach enables the dual complexities of marine ecosystems and multiple human pressures to be unravelled to identify and target issues effectively. The risk factor treatment linkage provides a platform to negotiate and develop effective management and research actions across jurisdictional, disciplinary, community and stakeholder boundaries.