Since Lewis and Clark navigated the upper Missouri River more than 200 years ago, the river has been engineered to control flooding and promote water traffic. These modifications have drastically changed the flow and character of the river and its floodplain and depleted and degraded habitat for birds and fish. For many years, environmentalists have urged the Army Corps of Engineers to assess the environmental impacts of its water management activities on the Missouri River and to lay the groundwork for reforms of its practices.

Among the reforms that environmentalists seek is an increase in the Missouri River's water flows during the months of May and June. River scientists argue that this increase would provide a vital reproductive trigger for native fish such as catfish, walleye, and the endangered pallid sturgeon, and would also help build sandbars to provide habitat for the endangered interior least tern and the threatened piping plover.

The Army Corps has proposed revisions to its master manual for water control that are supported by environmentalists. However, during consideration of H.R. 4733, the Fiscal Year 2001 Energy and Water Development appropriations bill, Senator Kit Bond (R-MO) inserted a rider to block revisions to the master manual and other proposed conservation actions on the river.

Senators Thomas Daschle (D-SD) and Max Baucus (D-MT) offered an amendment to strike the Bond rider from the Energy and Water appropriations bill. On September 7, 2000, the Senate rejected the amendment, 45–52 (Senate roll call vote 232). YES is the pro-environment vote. The House/Senate conference on the bill retained the Bond rider and the President vetoed the bill. Although the House voted to override the veto, the Senate did not have sufficient votes to do so and Senate leaders, in negotiations with the White House, agreed to drop the rider from the bill.