The global human population is growing exponentially, close to a majority lives and works near the coast, and coastal commerce and development are critical to the economies of many nations. Hence, coastal areas will continue to be a major focus of development and economic activity. People desire the economic advantages provided by coastal development along with the fisheries and social commodities supported by estuarine and coastal ecosystems. Because of these facts, we view the challenge of balancing coastal development with enhancing nearshore marine and estuarine ecosystems (i.e., net ecosystem improvement) as the top priority for coastal researchers in this century. Our restoration research in Pacific Northwest estuaries and participation in nearshore project design and impact mitigation has largely dealt with these competing goals. To this end, we have applied conceptual models, comprehensive assessment methods, and principles of restoration ecology, conservation biology, and adaptive management to incorporate science into decisions about uses of estuarine systems. Case studies of Bainbridge Island and the Columbia River demonstrate the use of objective, defensible methods to prioritize tidally influenced shorelines and habitats (i.e., riparian forests, marshes, unvegetated flats, rocky shores, seagrass meadows, kelp forests) for preservation, conservation, and restoration. Case studies of Clinton, Washington, and Port Townsend, Washington, demonstrate the incorporation of an ecological perspective and technological solutions into design of overwater structures to minimize impacts on nearshore ecosystems. Adaptive management has allowed coastal development and restoration uncertainties to be better evaluated, with the information used to improve management decisions. Although unproven on a large scale, we think these kinds of methods can contribute to the net improvement of already degraded ecosystems. The ingredients include applied science to understand the issues, education, incentives, empirical data, cumulative impact analysis, and an effective adaptive management program. Because the option of net ecosystem improvement is often more costly than alternatives such as no net loss, commitment by the local or regional community to this approach is essential.