Continental shelves and the waters overlying them support numerous industries as diverse as tourism and recreation, energy extraction, fisheries, transportation, and applications of marine bio-molecules (e.g., agribusiness, food processing, pharmaceuticals). Although these shelf ecosystems exhibit impacts of climate change and increased human use of resources (Halpern et al., 2012; IPCC, 2013, 2014; Melillo et al., 2014), there are currently no standardized metrics for assessing changes in ecological function in the coastal ocean. Here, we argue that it is possible to monitor vital signs of ecosystem function by focusing on the lowest levels of the ocean food web. Establishment of biodiversity, biomass, and primary productivity baselines and continuous evaluation of changes in biological resources in these economically and ecologically valuable regions requires an internationally coordinated monitoring effort that fully integrates natural, social, and economic sciences to jointly identify problems and design solutions. Such an ocean observing network is needed to protect the livelihoods of coastal communities in the context of the goals of the Future Earth program (Mooney et al., 2013) and of the Intergovernmental Platform on Biodiversity and Ecosystem Services (http://www.ipbes.net). The tools needed to initiate these assessments are available today.