Evidence that the earth’s climate is changing is overwhelming, and because climate affects temperature, patterns of circulation and chemistry of the ocean, marine ecosystems are changing as well. Effectively reducing climate-related threats requires management responses that move beyond disjointed efforts and that integrate diverse management actions with the goal of increasing adaptive capacity. The development of robust indicators—quantitative measurements that provide insight into the state of natural and socio-economic systems—is a necessary step toward these goals because indicators provide information that allows management strategies to be evaluated and refined. In this paper, we outline an approach to indicator selection that melds social and natural science. Our approach acknowledges that the value of specific indicators to policy makers and resource managers can diverge from the scientific value of these indicators. In addition, it is grounded in rigorous scientific analyses that meet widely accepted guidelines for ecosystem indicators. Our approach also recognizes that a suite of indicators is needed, and we argue that the optimal portfolio of indicators is one that ensures appropriate scientific information is captured while also maximizing the value of the indicators for policy makers. We contend that integrating natural and social science is crucial as we begin to recognize the potential consequences of climate change on marine ecosystems and seek ways to adapt existing management strategies to alternative futures.