This paper discusses the historic and contemporary challenges in the management of the lower Mississippi River Basin, and describes the evolving role of the federal government in addressing these challenges. In the early eighteenth century, the federal government was responsible for maintaining a navigable channel. After repeated calls by states for federal assistance with flood control and a devastating flood in 1927, the federal government additionally became the primary body responsible for protecting the Delta from floods. Although the resulting flood control system provided greater protection, it also brought new challenges, such as an increasingly large hypoxic zone in the Gulf of Mexico, land subsidence in southern Louisiana and water quality issues. The confluence of these environmental concerns and changing national values have once again broadened the scope of federal responsibility to include environmental management and ecosystem restoration, along with its original involvement in navigation and flood control. This triad of responsibility carries with it often-competing objectives that must be balanced within legal and institutional constraints, most notably a deficit of available funding for inland waterway projects and what appears to be a lack of political will for continued investment in the maintenance of existing and development of new projects.