Charles Merriam was born in Hopkinton, Iowa, on November 15, 1874, to Charles Edward Merriam and Margaret Campbell Kirkwood Merriam. The Merriams traced their lineage to Scottish immigrants who settled in Massachusetts in 1638. The father moved to Iowa in 1855, and served with the 12th Iowa Infantry Regiment in the American Civil War. Charles and Margaret (both Presbyterians) were married in 1868. Charles E. Merriam Sr. owned a dry goods store and was postmaster and president of the school board in Hopkinton. Charles Jr.'s elder brother was John C. Merriam (who became a noted paleontologist), and he had a younger sister, Susan Agnes Merriam.