Local Modifications to Federal Flood Control Projects Act of 2012 - Amends the Rivers and Harbors Appropriation Act of 1899 to direct the Secretary of the Army, upon the recommendation of the Chief of Engineers, to grant permission to a local sponsor to construct an improvement to a flood control project in accordance with this Act.
Authorizes the Secretary to grant permission for such an improvement: (1) that is necessary for the project to provide a qualified level of protection when, in the Secretary's judgment, the proposed improvement does not permanently reduce the existing level of protection; or (2) that is associated with permanently increasing the level of protection provided by the project from the authorized level or permanently realigning the project to substantially increase or otherwise significantly alter the geographic area protected by the project when, in the Secretary's judgement, the improvement does not adversely affect the existing level of protection and does not transfer the hydraulic impact of the project beyond the standards that the Chief of Engineers applies to projects proposed for initial federal authorization. Defines "qualified level of protection" as the lesser of the authorized level or the level necessary to receive, maintain, or restore accreditation pursuant to the National Flood Insurance Act of 1968. Prohibits the Secretary from granting permission regarding such an improvement unless it is constructed in accordance with plans and specifications prepared and certified by a registered professional engineer.
Sets forth: (1) requirements for submission of an improvement application, (2) deadlines for action on such an application, (3) approval and disapproval procedures, and (4) procedures for administrative and judicial appeals of the disapproval of an application. Directs the Secretary to issue guidelines to facilitate and expedite the review of proposed improvements.