We study the environmental regulation of industrial activities that are organized as projects. Applications arise in construction, ship and aircraft building, and film making, among other industries. Relative to manufacturing, environmental regulation is different in project‐based industries, due to the uniqueness and geographical diversity of projects, and a lack of product takeback programs. Because the amount of waste and pollution generated by project companies can be large, regulators need environmental policies to ensure reduction of waste and pollution. We consider a regulator who attempts to maximize social welfare. We model this problem as a bilevel nonlinear program. The upper level regulator specifies waste reduction targets, which the lower level project companies meet using waste stream reduction and remediation of pollution, while attempting to control their project costs. We find that high waste diversion targets lead to outcomes with little pollution, but excessive project costs and only modest waste stream reduction. Projects that have lower task precedence density, or that have pollutants with different environmental impacts, show larger increases in project cost and time resulting from regulation. We describe a subsidy for waste stream reduction that coordinates the system, and we estimate the value of coordination. We also describe a bonus that encourages truthful reporting by project companies, and evaluate the relative cost and effectiveness of the subsidy and the bonus. © 2015 Wiley Periodicals, Inc. Naval Research Logistics 62: 228–247, 2015