Lower Colorado River Protection Act - Establishes: (1) the Lower Colorado River Management Conference to develop a Lower Colorado River Pollution Elimination and Ecosystem Restoration Plan, and (2) the Lower Colorado River Protection Program within the Environmental Protection Agency (EPA) Region 9 office to provide staff and support services to the Conference.

Directs the Administrator of EPA, acting through the Director of such Program, to establish a multidisciplinary environmental research program for the Lower Colorado River. Authorizes the Administrator to make grants to conduct environmental and pollution control projects in the River Basin.

Requires the Conference to publish such Plan within two years. Sets forth provisions regarding Plan contents, public review, and approval. Authorizes the Administrator to make grants for work necessary for Plan development. Requires the Program Director, after Plan approval, to take specified steps to implement it, including providing multiagency oversight and coordination.

Authorizes the Administrator, through the Director, to carry out qualified projects to monitor or evaluate the release or discharge of pollutants in the Lower Colorado River Basin, to prevent, reduce, or eliminate pollution in the River, or to restore or maintain the ecosystem health of the River in accordance with the Plan. Directs the Administrator to develop a list of existing federal programs that are authorized to conduct projects that fit such qualified project requirements and to work with the responsible agencies to avoid committing resources under this Act to projects other programs will implement.

Requires the Secretary, in cooperation with the Colorado River Regional Sewer Coalition or other regional or local entities, to participate in the planning, design, and construction of systems for municipal wastewater treatment.