According to the United States Census Bureau, the city has a total area of 5.2 square miles (13.4 km2), of which 3.5 square miles (9.0 km2) is land and 1.7 square miles (4.5 km2), or 33.19%, is water.
Chuathbaluk was the site of an Deg Xinag Indian summer fish camp in the mid-19th century. The village has been known as Chukbak, St. Sergius Mission, Kuskokwim Russian Mission, and Little Russian Mission. The village was often confused with Russian Mission on the Yukon, so in the 1960s the name was changed to Chuathbaluk, which is derived from the Yup'ik word Curapaluk, meaning "Home of the Big Blueberries." The Russian Orthodox Church built the St. Sergius Mission by 1894, and residents of Kukuktuk from 20 miles (32 km) downriver moved to the mission. Much of the village was lost in an influenza epidemic in 1900. By 1929, the site was deserted, although Russian Orthodox members continued to hold services at the mission. In 1954, the Crow Village Sam Phillips family from Crow Village resettled the mission, and were joined later by individuals from Aniak and Crooked Creek. The church was rebuilt in the late 1950s, and a state school opened in the 1960s. The city was incorporated in 1975.