St. Mary Diversion and Conveyance Works and Milk River Project Act of 2006

St. Mary Diversion and Conveyance Works and Milk River Project Act of 2006 - Directs the Secretary of the Interior to conduct studies to determine: (1) the feasibility of rehabilitating and improving the St. Mary Diversion and Conveyance Works (a portion of the Milk River Project, a Bureau of Reclamation project in Montana, that is located within the Blackfeet Reservation) to provide for sustained environmental and economic benefit within the St. Mary and Milk River basins; and (2) the environmental impact of such rehabilitation project.

Directs the Secretary to: (1) initiate the planning, design, and construction of the project alternative that is selected; and (2) develop and implement an emergency response plan to be followed in the event of a catastrophic infrastructure failure. Establishes in the Treasury an emergency response plan fund.

Requires: (1) the Milk River Project to be operated primarily for irrigation purposes; and (2) the Secretary to prioritize Project structures in need of rehabilitation and improvement.

Directs the Secretary to: (1) ensure that land and water rights held in trust for the benefit of the Blackfeet Tribe are protected; (2) resolve tribal claims against the United States; (3) identify appropriate Blackfeet projects to improve economic conditions on the Reservation; (4) complete studies to determine the feasibility of carrying out such projects; and (5) conduct studies to determine the feasibility of rehabilitating and improving Blackfeet irrigation project structures determined to be in need based on the appraisal investigation and of developing a safe and adequate rural, municipal, and industrial water supply project for the residents of the Fort Belknap Reservation and surrounding communities.