Directs the Secretary of the Army to operate the Missouri River mainstem reservoir system to minimize adverse environmental and economic impacts to authorized uses on the Missouri River and such system as long as such operation does not conflict with the Flood Control Act of 1944. Requires the Secretary, if an authorized use is being threatened with adverse impact by the operation of the system, to prevent or mitigate such impacts through operational changes if the environmental or economic impacts to a State or tribe outweigh potential adverse impacts arising from the preventive or mitigative action.

Authorizes a general appropriation to be deposited into a Missouri River Basin States damage fund to mitigate impacts incurred when operational adjustments have been denied or implemented.