On the night of 1 April 1862, he was the Navy commander of a combined Army-Navy boat expedition from St. Louis, which landed and spiked the guns of Fort No. 1 above the Confederate stronghold, Island No. 10. He was promoted to Acting Volunteer Lieutenant for gallantry in this expedition.
After joining in the bombardments of Vicksburg, he took command of Forrest Rose to patrol the Mississippi and its tributaries. On 15 February 1864, his gunboat repelled the attack of Confederate raiders, saving the town of Waterproof, Louisiana and its Federal garrison.
Lt. Johnston resigned from the naval service 23 June 1864. He died on 23 April 1912 at St. Louis.