North Bay Water Reuse Program Act of 2009

North Bay Water Reuse Program Act of 2009 - Amends the Reclamation Wastewater and Groundwater Study and Facilities Act to authorize the Secretary of the Interior, contingent upon a finding of feasibility and acting through a cooperative agreement with the state of California or a subdivision thereof, to enter into cooperative agreements with eligible entities in the North San Pablo Bay watershed located in Marin, Napa, Solano, and Sonoma Counties for the planning, design, and construction of water reclamation and reuse facilities and recycled water conveyance and distribution systems.

Directs the Secretary and such an entity to use the design work and environmental evaluations initiated by non-federal entities and the Corps of Engineers in that watershed to the maximum extent practicable.

Requires any such cooperative agreement to require the program to be carried out in two phases, during which the Secretary and an entity shall complete the planning, design, and construction of: (1) the main treatment and main conveyance systems; and (2) the sub-regional distribution systems.

Limits the federal share to 25% of the total cost of the first phase of the project. Allows the non-federal share to be in the form of in-kind services that the Secretary determines would contribute substantially toward the completion of the water reclamation and reuse project. Prohibits the Secretary from providing funds for operation and maintenance of the project.