The Water Resources Development Act (WRDA) of 1999 authorized annual appropriations of $33.17 million for the Upper Mississippi River Restoration (UMRR) Program; $22.75 million for Habitat Rehabilitation and Enhancement Project (HREP) element; $10.42 million for Long Term Resource Monitoring (LTRM) element.  Congress appropriates funds for UMRR as a single line item; from that annual program appropriation, funds are allocated for overall program management costs, as well as the two major program elements— i.e., HREPs and LTRM.  The authorization also allows UMRR the flexibility to transfer up to 20 percent of the annual appropriation between the two elements in reponse to changing funding levels and regional and national priorities. 

The annual appropriation averaged $21.388 million between FY 2004 and FY 2010, ranging from a low of $16.470 million to a high of $21.894 million.  In FY 2009, additional funding from the American Recovery and Reinvestment Act (ARRA) combined with regular appropriations to give UMRR $30.889 million in total funding.  The additional funding increased UMRR's capabilities substantially, allowing the program to expedite critical habitat restoration and research priorities.  Beginning in FY 2013, appropirations to the UMRR increased; and, for FY 2015, the full authorized amount of $33.17 million was identified in the President's budget. since then, funding levels have been lower; averaging around $20 million annually.

In administering the UMRR, the Corps transfers funding to U.S Geological Survey (USGS) to implement the LTRM element.  A portion of those funds is then provided to the states to support the work of the six field stations.  The Corps also transfers funding to the U.S. Fish and Wildlife Service to support its involvement in the planning, design, and monitoring of HREPs.

While appropriations to the Corps of Engineers fund the largest portion of UMRR costs, that amount does not fully reflect the investment that has been made.  The U.S. Fish and Wildlife Service is responsible for the costs of operating and maintaining HREPs on lands that it manages.  The five basin states have also made substantial investment in UMRR.  This includes non-Federal cost share for HREPs on non-refuge lands, operation and maintenance of the habitat projects on lands the states manage, and various efforts to support states’ involvement in planning, coordinating, and implementing all components of the UMRR.