Missouri River Enhancement and Monitoring Act of 2003

Missouri River Enhancement and Monitoring Act of 2003 - Directs the Secretary of the Interior, acting through the Biological Resources Division of the U.S. Geological Survey, to establish the Missouri River monitoring and research program to: (1) coordinate the collection of information on the biological and water quality characteristics of the Missouri River and evaluate how those characteristics are affected by hydrology; (2) coordinate the monitoring and assessment of biota (including threatened or endangered species) and habitat of the River; and (3) make recommendations on means to assist in restoring the River's ecosystem.

Designates the River Studies Center of that Division, located in Columbia, Missouri, to administer the program. Directs the Center to: (1) assist in the recovery of the threatened and endangered species of the River; (2) establish a scientific database; (3) enter into contracts with Indian tribes that have reservations along the River for activities supporting this Act; (4) provide financial assistance to the U.S. Fish and Wildlife Service and State agencies to monitor and recover threatened and endangered species; and (5) carry out a competitive grant program for research on the impacts of the operation and maintenance of the River's mainstem reservoirs on the health of fish and wildlife.

Requires the Center, the Directors of the Fish and Wildlife Service and of the Geological Survey, and the Missouri River Natural Resources Committee to: (1) prioritize research needs; (2) issue a request for grant proposals; and (3) award grants.

Directs the Governors of specified States and the governing bodies of the Indian tribes of the Missouri River Basin to establish a Missouri River Basin Stakeholder Committee to make recommendations to Federal agencies on means of restoring the River's ecosystem.