Mississippi River Navigation Sustainment Act - Directs the Chief of Engineers to carry out a study of the Mississippi River Basin to: (1) improve the coordinated and comprehensive management of water resource projects in the greater Mississippi River Basin relating to extreme weather conditions, and (2) evaluate the feasibility of modifications to those projects and develop new projects to improve the reliability of navigation and more effectively reduce flood risk.

Directs the Chief to improve forecasting on the Mississippi River by: (1) updating forecasting technology deployed on the River and its tributaries, (2) constructing additional sedimentation ranges on the River and tributaries, and (3) deploying additional automatic identification system base stations at river gage sites. Requires the Chief to prioritize the sections of the River on which additional and more reliable information would have the greatest impact on maintaining navigation.

Authorizes the Chief to: (1) construct, operate, and maintain ingress and egress paths to docks, loading facilities, fleeting areas, and other critical locations outside of the authorized navigation channel on the Mississippi River upon determining such actions to be critical to maintaining safe and reliable navigation; and (2) mitigate, through dredging, any incidental impacts to loading or fleeting areas outside of such channel that result from operation and maintenance of the channel.

Directs the Chief: (1) in accordance with the project for navigation, Mississippi River between the Ohio and Missouri Rivers (Regulating Works), Missouri and Illinois, to carry out a 10-year pilot program to restore and protect fish and wildlife habitat in the middle Mississippi River; and (2) as part of such program, to conduct activities necessary to improve navigation through such project while restoring and protecting fish and wildlife habitat.