A great diversity of organisms modify the physical structure of estuarine and coastal environments. These physical ecosystem engineers–particularly, dune and marsh plants, mangroves, seagrasses, kelps, reef-forming corals and bivalves, burrowing crustaceans, and infauna–often have substantive functional impacts over large areas and across distinct geographic regions. Here, we use a general framework for physical ecosystem engineering to illustrate how these organisms can exert control on sedimentary processes, coastal protection, and habitat availability to other organisms. We then discuss the management implications of coastal and estuarine engineering, concluding with a brief prospectus on research and management challenges.