Pitting the dynamicism and uncertainty inherent in undisturbed coastal ecosystems against the stability and predictability required of human-dominated landscapes creates the paradox of the dual mandate. We describe a gradient of estuarine types ranging from systems that experience little human intrusion—conservation estuaries—to those that are dominated by people or extractive uses—production and urban-industrial estuaries. Future approaches to managing these estuarine resources will require a division of the concept of marine protected areas into at least two subcategories: “conservation” managed areas (CConservationMAs) and “commerce” managed areas (CCommerceMAs). The latter includes conditions where humans are not only a core feature of the landscape but also where extractive uses drive a large part of the local, regional, and even national economy. System reliability and predictability of ecosystem services are integral components of any management scheme in CCommerceMAs. By recognizing this division managers can construct appropriate baselines that encompass the biodiversity and ecological integrity inherent in relatively undisturbed estuaries (or portions thereof), or the ecosystem health and system reliability that characterize urban-industrial systems. The terms ecosystem restoration and ecosystem rehabilitation are also distinguished; the former term is used to describe practices that return ecosystems to optimum biological integrity, whereas the latter term is applied to the health of human-dominated estuaries where the goal is to manage natural processes and functions. Our proposed approach does not mean that ecosystem quality is sacrificed in urban-industrial or production systems; to the contrary, contaminant source control, suitable sediment and water quality, and the human endeavors to address them are just as important to sustaining commercial activity as they are to the well-being of extant biota. So too, are the conservation and preservation of existing critical habitat (proximate reservoirs of biodiversity) in urban-industrial systems, and rehabilitation of habitats that support species coadapted to the presence of humans.