An ecosystem-based approach to bivalve aquaculture management is a strategy for the integration of aquaculture within the wider ecosystem, including human aspects, in such a way that it promotes sustainable development, equity, and resilience of ecosystems. Given the linkage between social and ecological systems, marine regulators require an ecosystem-based decision framework that structures and integrates the relationships between these systems and facilitates communication of aquaculture–environment interactions and policy-related developments and decisions. The Drivers-Pressures-State Change-Impact-Response (DPSIR) management framework incorporates the connectivity between human and ecological issues and would permit available performance indicators to be identified and organized in a manner that facilitates different regulatory needs. Suitable performance indicators and modeling approaches, which are used to assess DPSIR framework components, are reviewed with a focus on the key environmental issues associated with bivalve farming. Indicator selection criteria are provided to facilitate constraining the number of indicators within the management framework. It is recommended that an ecosystem-based approach for bivalve aquaculture be based on a tiered indicator monitoring system that is structured on the principle that increased environmental risk requires increased monitoring effort. More than 1 threshold for each indicator would permit implementation of predetermined impact prevention and mitigation measures prior to reaching an unacceptable ecological state. We provide an example of a tiered monitoring program that would communicate knowledge to decision-makers on ecosystem State Change and Impact components of the DPSIR framework.