Great Lakes Navigation System Sustainability Act of 2013 - Directs the Secretary of the Army, acting through the Chief of Engineers, to manage and allocate funding for all commercial and recreational navigation projects in the Great Lakes Navigation System as components of a single system, recognizing the interdependence of the projects.
Directs the Secretary, acting through the Chief of Engineers, to: (1) establish a program to fund eligible operations and maintenenace projects of the System to their authorized depths and widths, and (2) give higher priority to projects at certain harbors in which a 50% non-federal share of costs of eligible operations and maintenance expenses is provided.