Charles S. Stewart was born aboard the US ship Thames on April 11, 1823 while the Thames was at sea in the Pacific Ocean. His mother was Harriet Bradford Stewart, and his father, Reverend Charles Samuel Stewart was a US Navy chaplain. Stewart's ancestors included great-grandfather Charles Stewart. Stewart was raised and educated in Cooperstown, New York and Princeton, New Jersey. At age 17, Stewart began the first of three sea journeys as the captain's clerk aboard the U.S.S. Brandywine. In 1842, he began attendance at the United States Military Academy. Stewart graduated in 1846, ranked first of the 59 students in his class, which entitled him to a coveted assignment in the Corps of Engineers.
After the war, Stewart was superintending engineer of the defenses of the Delaware River and Delaware Bay. From 1870 to 1886, he was a member of the board of engineers that planned the defenses of the Pacific Coast, a duty he carried out while serving as superintending engineer of construction of Fort Point, Point San Jose, and Angel Island in San Francisco Harbor. In 1872, Stewart supervised the removal of Rincon Rock from San Francisco Harbor. In 1872 and 1872, he led the team that examined the seawalls and breakwaters at Trinidad Harbor, Santa Cruz, and Estero Bay. Between 1873 and 1886, Stewart was superintending engineer of construction of the fort at San Diego, leader of the team that examined the estuary in Santa Barbara Channel, and the team that surveyed the San Joaquin River below Stockton. In 1874 and 1875, he supervised the removal of the wreck of the SS Patrician and the outcropping known as Noonday Rock from San Francisco Harbor. Between 1875 and 1886, Stewart oversaw improvements to the harbor in San Diego Bay, and the San Joaquin River. He also oversaw the survey of the Colorado River between Fort Yuma and Dorado Canyon in 1879, examination of the harbors of San Luis Obispo, San Buenaventura, and Santa Barbara in 1879, and survey of Trinidad Harbor from 1879 to 1880. From 1880 until his retirement, Stewart was chief engineer of the 12thLighthouse District, examined and surveyed the channel for San Diego Harbor, constructed a breakwater for the San Luis Obispo Harbor, and served on several engineer boards that planned River and Harbor Improvements.
Retirement and death
Stewart was promoted to colonel in June 1882. He retired in 1886, and lived in Cooperstown. In 1904, he was promoted to brigadier general on the retired list in recognition of the superior service he rendered throughout his career. he died in Siasconset, Massachusetts on July 22, 1904 and was buried at Lakewood Cemetery in Cooperstown.