The longest-serving acting defense secretary will be nominated to do the job permanently, White House officials announced.
The Defense Department continues to address concerns that firefighting foam is polluting groundwater.
A Pentagon sexual-assault task force has made a number of recommendations to curb the crime in the ranks.
Shanahan abruptly canceled plans to travel to Europe, citing the crisis in Venezuela and the situation along the border.
The academy announced Thursday that Shanahan will address the graduating class in Annapolis, Maryland, on May 24.
Acting Defense Secretary Patrick Shanahan did not use his position to promote Boeing, the Pentagon's top watchdog said.
Shanahan has been serving as the interim Pentagon chief since Jan. 1, after Jim Mattis resigned.
The task force will assess how the armed forces handle and prosecute sex crimes.
Lawmakers on Thursday indicated they remained skeptical of the Pentagon's latest proposal to stand up a U.S. Space Force.
Citizens for Responsibility and Ethics in Washington filed the request alleging Shanahan violated rules by promoting Boeing.