After years in other states he settled down with his wife Margaret (1820–1908) at his town at the foot of Mount Diablo, where he and his family prospered.

Joel Clayton and Charles Rhine cofounded the town, and each wanted to name it after himself.

Joel and his wife Margaret both died in Clayton, and were buried in Live Oak Cemetery in what is now Concord, CA.

[8] Clayton prospered during the coal mining boom in eastern Contra Costa County.

After steady expansion during the 1970s to the east and west from its original boundaries, Clayton's land area more than doubled in 1987 to near its present-day boundaries with the annexations of the Dana Hills/Dana Ridge and Clayton Wood subdivisions, as well as the former Keller Ranch property that was developed during the 1990s with the Oakhurst Country Club.

Wildfires have been a common occurrence in recent years as California had a major drought from 2011-2017.

Evacuations were ordered for several areas, including Oak Hill Lane and Curry Canyon.

Full containment was announced on September 14, 2013, having burned 3,100 acres (4.8 sq mi; 1,300 ha).

[10] On July 25, 2018, a vegetation fire broke out on Marsh Creek Rd near Morgan Territory.

According to the United States Census Bureau, the city has a total area of 3.8 square miles (9.8 km2), all land.

[16] The public schools which the K-12 students of Clayton attend include: Mt.