It was Johnston who was instrumental in the development of the Alcatraz Federal Penitentiary as a prison and was involved in the design of it as a federal prison in 1934. He served as the first warden of Alcatraz from 1934 until 1948. He was considered to be a highly strict disciplinarian and a devout reformist who imposed a number of rules upon the prison including a strict code of silence, which led to him being nicknamed the 'Golden Rule Warden' from his San Quentin days. However, he was relatively popular among inmates and guards, known as "Old Saltwater" to the inmates, and is credited with challenging the barbaric tactics used in the prison when he was there, including strait jackets and solitary confinement in darkness and working towards the general improvement of the lives of prisoners. In 1937 he was attacked by Burton Phillips from behind in the Dining hall who beat him in anger at a worker's strike, but he continued to attend meals unguarded. Ten of the fourteen escape attempts took place when he was warden, including the one that resulted in the Battle of Alcatraz. Johnston wrote several books during his lifetime including "Prison Life is Different" where he documents his time spent as warden at Folsom, San Quentin, and Alcatraz. He was married to Ida Mae Fulton and had one son and three daughters.