North Bay Water Reuse Program Act of 2006

North Bay Water Reuse Program Act of 2006 - Authorizes the Secretary of the Interior to offer to enter into cooperative agreements with eligible entities in the North San Pablo Bay watershed located in Marin, Napa, Solano, and Sonoma Counties, California, for the planning, design, and construction of water reclamation and reuse projects.

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 such an agreement to specify the responsibilities of the Secretary and the entity regarding: (1) cost-share requirements; (2) needs assessment and project planning and design; (3) environmental compliance activity; (4) facilities construction; and (5) construction contract administration.

Requires that any such project consist of two phases, during which the Secretary and an entity shall complete the planning, design, and construction of: (1) the main treatment and main conveyance system; and (2) the sub-regional distribution systems.

Authorizes the Secretary to provide financial and technical assistance to an entity in planning, designing, conducting related pre-construction activities for, and constructing a project. Makes the entity responsible for the annual operation, maintenance, and replacement costs of the project. Requires the entity to develop an operation, maintenance, and replacement plan for the project.