Stop Invasive Species Act - Directs the Secretary of the Army, acting through the Chief of Engineers, to: (1) expedite a feasibility study under the Water Resources Development Act of 2007 on the range of options and technologies available to prevent the spread of aquatic nuisance species (including Asian carp) between the Great Lakes and Mississippi River Basins through the Chicago Sanitary and Ship Canal and other aquatic pathways; and (2) if the project is justified, proceed directly to project preconstruction engineering and design.
Requires the report on the study to focus on: (1) such prevention as the permanent hydrological separation of the Great Lakes and Mississippi River Basins, and (2) specified watersheds of rivers and tributaries in Illinois and Indiana associated with the Chicago Area Waterway System (CAWS).
Defines "hydrological separation" as a physical separation on the CAWS that would disconnect the Mississippi River watershed from the Lake Michigan watershed and prevent the transfer of all aquatic species between such bodies of water.
Requires, within 90 days after enactment of this Act, an interim report to Congress on milestones that will be met prior to final completion of the study. Requires the final report to be completed within 18 months.