Platte River Recovery Implementation Program and Pathfinder Modification Authorization Act of 2006

Platte River Recovery Implementation Program and Pathfinder Modification Authorization Act of 2006 - Authorizes the Secretary of the Interior, acting through the Commissioner of Reclamation and in cooperation with the Governance Committee established under the Platte River Recovery Implementation Program Cooperative Agreement, to: (1) participate in such Program; (2) carry out any projects or activities that are designated for implementation during the Program's first 13 years (First Increment); (3) acquire interests in land, water, and facilities from willing sellers; (4) transfer acquired interests; and (5) accept or provide grants.

Allows the Program to be modified before the completion of the First Increment if the Secretary and the states of Nebraska, Wyoming, and Colorado determine that the modifications are consistent with program purposes. Terminates the Secretary's authority to implement the First Increment on September 30, 2020.

Authorizes the Secretary, acting through the Commissioner, to: (1) modify the Pathfinder Dam and Reservoir; and (2) enter one or more agreements with the state of Wyoming to implement the Pathfinder Modification Project. Authorizes the capacity of the Pathfinder Reservoir to be used for municipal, environmental, and other purposes, as described in Appendix F to the final settlement stipulation in Nebraska v. Wyoming.