Cormorant Management and Natural Resources Protection Act - Amends the Migratory Bird Treaty Act to delegate the authority of the Secretary of the Interior under such Act with respect to double-crested cormorants (Phalacrocorax auritus) to a state on the date the Secretary approves a cormorant management plan submitted by such state.

Requires the Secretary to: (1) approve or disapprove a management plan within 60 days of the plan's submission, (2) approve such plan if it is in accordance with U.S. obligations under treaties and federal law, (3) provide to the relevant governor the reasons for disapproving a plan and an opportunity to revise and resubmit the plan, (4) review each approved state management plan every five years, and (5) revoke such approval and delegation if the plan or the governor's exercise of delegated authority is not in accordance with such Act or any treaty implemented by such Act. Deems a management plan approved if the Secretary doesn't approve or disapprove it within 60 days after submission.

Applies an approved management plan in lieu of regulations issued under such Act.

Requires the Secretary to conduct educational and informational activities for the owners and operators of aquaculture facilities to improve their efforts to prevent cormorants from consuming aquatic species being reared in such facilities.