The goal of ecosystem-based management (EBM) is to support a sustainable and holistic multisectored management approach, and is recognized in a number of international policy frameworks. However, it remains unknown how these goals should be linked to assessments and management plans for marine fauna, such as mammals and fish stocks. It appears particularly challenging to carry out trade-off analyses of various ocean uses without a framework that integrates knowledge of environmental, social, and economic benefits derived from nonstationary marine fauna. We argue this gap can be filled by applying a version of the ecosystem-service approach at the population level of marine fauna. To advance this idea, we used marine mammals as a case study to demonstrate what indicators could operationalize relevant assessments and deliver an evidence base for the presence of ecosystem services and disservices derived from marine mammals. We found indicators covering common ecosystem service categories feasible to apply; examples of indicator data are already available in the literature for several populations. We encourage further exploration of this approach for application to marina fauna and biodiversity management, with the caveat that conceptual tensions related to the use of the ecosystem service concept itself needs to be addressed to ensure acceptance by relevant stakeholders.