In the Maryland Campaign, at South Mountain, he led a bayonet charge that resulted in taking the enemy position, and also fought at the Battle of Antietam.

After that disastrous defeat, he and other generals journeyed to see President Abraham Lincoln and informed him of their lack of confidence in Army of the Potomac commander, Maj. Gen. Ambrose E. Burnside.

After the capture of Atlanta, Newton left active field duty and commanded the District of Key West and the Tortugas of the Department of the Gulf from 1864 to 1866.

His last campaign resulted in a defeat at the Battle of Natural Bridge in Florida in March 1865, which temporarily enabled the Confederates to hold on to the state capital.

Returning to the Corps of Engineers, Newton oversaw improvements to the waterways around New York City, into Vermont, and to the Hudson River above Albany.

This work is covered in detail in the 2021 book by Thomas Barthel Opening the East River: John Newton and the Blasting of Hell Gate.

[5] In 1899, the Corps of Engineers named a 175-foot paddlewheeler in Newton's honor; the boat was later used as the Minnesota Centennial Showboat until its destruction by fire in 2000.