Eastern New Mexico Rural Water System Act of 2006 - Authorizes the Secretary of the Interior to provide financial and technical assistance to the Eastern New Mexico Rural Water Authority to assist in planning, designing, conducting preconstruction activities for, and constructing the Eastern New Mexico Rural Water System.
Limits the federal share of the cost of any activity to 75%. Provides that the total cost of the System shall include any costs incurred by the Authority on or after October 1, 2003, for System development.
Makes the Authority responsible for annual operation, maintenance, and replacement costs. Directs the Authority to develop an operation, maintenance, and replacement plan that establishes rates and fees necessary to ensure that the System is properly maintained and capable of delivering approximately 16,500 acre-feet of water per year. Prohibits the use of funds under this Act until such plan is developed and until the Secretary and the Authority have complied with applicable requirements of the National Environmental Policy Act of 1969. Directs the Secretary to consult with the New Mexico Interstate Stream Commission and the Authority in preparing any required biological assessment under the Endangered Species Act of 1973.