Mni Wiconi Project Act Amendments of 2012

Mni Wiconi Project Act Amendments of 2012 - Amends the Mni Wiconi Project Act of 1988 to include within the service area of the Oglala Sioux Rural Water Supply System the tract of land in Nebraska set aside as part of the Pine Ridge Indian Reservation by the executive order dated February 20, 1904.

Directs the Secretary of the Interior (the Secretary) to develop separate plans for completing, and enter into agreements with specified agency heads to complete, the Oglala Sioux Rural Water Supply System, the Rosebud Sioux Rural Water Supply System, and the Lower Brule Sioux Rural Water Supply System, in consultation with specified federal agencies and the Oglala Sioux Tribe, the Rosebud Sioux Tribe, and the Lower Brule Sioux Tribe, respectively. Requires: (1) the Director of the Bureau of Indian Affairs (BIA) to assist the Secretary in completing such Systems by constructing, repairing, and upgrading plumbing fixtures, skirting, and other necessary features to ensure that houses within the service areas are able to meet the standards for connecting to such Systems; and (2) the Secretary and the Secretary of Agriculture to complete, within 15 years, the livestock distribution systems for the Oglala Sioux Rural Water Supply System and the Rosebud Sioux Rural Water Supply System consistent with the Final Engineering Report dated May 1993.

Directs the Secretary, in cooperation with South Dakota, all Indian tribes residing on reservations within that state, and other federal agencies, to submit by January 2014 recommendations for financing and implementing mitigation plans for: (1) fish and wildlife and terrestrial losses, including the loss of Native American cultural resources, resulting from the construction and operation of the Oahe Dam and Reservoir, Big Bend Dam and Reservoir, and Fort Randall Dam and Reservoir; and (2) fish and wildlife and terrestrial losses and any impacts to groundwater resulting from the construction and operation of the dams and reservoirs on the Missouri tributaries within South Dakota.

Authorizes appropriations under such Act for planning, design, and construction and for operation and maintenance of such Systems.

Requires such Tribes to update and complete required feasibility studies beginning for FY2012.

Adds provisions (entitled the Mni Wiconi Project Emergency Assistance Planning Act of 2012) to: (1) require the Secretaries of the Interior, Defense (DOD), and Homeland Security (DHS) to develop and implement a five-year plan to meet the needs of the Mni Wiconi Project Rural Water Systems in emergency situations, and (2) establish in the Treasury the Mni Wiconi Emergency Assistance Fund.