Barrier Project Consolidation and Construction Act of 2006 - Considers the Chicago Sanitary and Ship Canal Dispersal Barrier Project (Barrier I) and the project related to the Chicago Sanitary and Ship Canal Dispersal Barrier (Barrier II) to constitute a single project to prevent the spread of aquatic nuisance species.
Directs the Secretary of the Army, through the Chief of Engineers, to: (1) upgrade and make permanent Barrier I; (2) construct Barrier II; (3) operate and maintain Barriers I and II as a system; (4) study options and technologies for reducing the impacts of hazards that may reduce the Barriers' efficacy; and (5) provide each state with a credit equal to the amount of funds contributed by the state toward Barrier II.
Directs the Secretary to: (1) study options and technologies to prevent the spread of aquatic nuisance species between the Great Lakes and Mississippi River Basins through the Chicago Sanitary and Ship Canal and other aquatic pathways; and (2) determine the the feasibility of, and construct and maintain if found feasible, a dispersal barrier project at the Lake Champlain Canal.