Nitrogen compounds are among the principal constituents of concern in aquatic systems because of their role in eutrophication, and their impacts on aquatic invertebrate and vertebrate species. Nitrogen compounds also augment plant growth, which in turn stimulates the biogeochemical cycles of the wetland. The wetland nitrogen cycle is very complex, and control of even the most basic chemical transformations of this element is a challenge in ecological engineering. This chapter describes the wetland nitrogen cycle, summarizes current knowledge about environmental factors that control nitrogen transformations, and provides approaches that can be used to design wetland treatment systems to treat nitrogen.