Harbors and waterways are a significant part of the nation's transportation system. Because of the national economic benefits of maritime transport, the federal government has invested in navigation infrastructure for two centuries. The future direction of federal financing of the system, however, remains uncertain. A recent proposal by the Bush Administration and proposed legislation are in opposite directions: the Administration proposed reducing the navigation system's draw on general revenue funds, while H.R. 2557 (passed by the House, September 24, 2003) could increase federal investment in the nation's harbors. There are also many other areas of debate, such as how to balance navigation uses and other river uses and how to improve the efficacy and environmental sensitivity of federal investments. Moreover, there is much debate over individual projects and the planning processes used to justify them. This report outlines the commercial navigation system, how the federal government finances the system, some of the proposals to change federal financing, and current challenges to the future of harbors and inland waterways. The contentious policy issues related to the harbor maintenance tax are not addressed in this report; see CRS Report RL31264, Harbor Maintenance Funding, by John F. Frittelli. This report will be updated as developments warrant.