Building with Nature is a new approach to designing water infrastructure, one that seeks to realize socioeconomic project goals in harmony with the environment. The Dutch dredging industry is promoting its application in the Netherlands, but similar concepts are emerging internationally. The Working with Nature concept has been developed under the auspices of the World Association for Waterborne Transport Infrastructure, Engineering with Nature by the US Army Corps of Engineers, and Flanders Bays 2100 by a group of Belgian dredging companies and international consultants. The research discussed in this article focuses on the feasibility of implementing the Building with Nature approach in the context of EU Natura 2000 governance. The initial expectation of the industry was that Natura 2000 regulations would obstruct innovative Building with Nature attempts. The empirical evidence points to a shift toward Building with Nature have taken place on the governance and project levels, and the goals of Natura 2000 and Building with Nature converging in practice. Using specific project-level variables identified by researchers, guidance for project development in Natura 2000 areas was proposed. We conclude by discussing the implications of the research results for the dredging industry dealing with Natura 2000 regulations in Europe and similar overarching nature regulations elsewhere.