Mississippi River Protection and Restoration Act of 2004

Mississippi River Protection and Restoration Act of 2004 - Amends the Upper Mississippi River Management Act of 1986 to: (1) allow interagency agreements under such Act between the Secretary of the Army (the Secretary) and the Secretary of the Interior to provide for maintenance of completed projects on Federal lands; (2) direct the Secretary to establish an independent science (currently, technical) advisory committee; (3) require such committee to include scientists, hydrologists, and engineers and to review and provide public comment on project criteria, selection, and sequencing; and (4) direct the Secretary to develop a system to rank proposed projects.

Amends the Water Resources Development Act of 1986 to: (1) increase the authorization of appropriations; (2) make project costs a Federal responsibility; (3) require a non-Federal sponsor to share 35 percent of the cost of projects constructed on private land; and (4) authorize the Secretary to share the cost of riverfront projects.

Establishes the Upper Mississippi Trust Fund and a charitable and nonprofit corporation to administer funds and gifts. Authorizes the use of Trust funds for aquatic and floodplain habitat restoration, riverfront revitalization, and administrative costs. Directs the Science Advisory Board to annually review projects proposed by the Board of Trustees.

Directs the Secretary to establish: (1) at the Waterways Experiment Station in Vicksburg, Mississippi, a program to coordinate monitoring and research in the Mississippi River Basin; and (2) a consortium of universities to demonstrate the full range of wetland values and functions, to reduce nutrient loadings to the Gulf of Mexico, and to sequester carbon.