He was born in Hopkinton, Iowa, the eldest child of postmaster, store proprietor, and American Civil War veteran Charles E. Merriam.

As a young man, he began collecting Paleozoic invertebrate fossils near his Iowa home.

He received a bachelor's degree from Lenox College in Hopkinton, Iowa, his father's alma mater, then went to the University of California to study geology and botany under Joseph Le Conte.

In 1894 he returned to the U.S. and joined the faculty at the University of California, teaching and performing research in both vertebrate and invertebrate paleontology.

In 1901 one of his lectures on paleontology inspired the young Annie Montague Alexander, who financed and took part in his expedition that year to Fossil Lake in Oregon.

In 1903 he was recognized as an Associate Member of the Boone and Crockett Club, a wildlife conservation organization founded in 1887 by Theodore Roosevelt and George Bird Grinnell.

A biography, which details his efforts to preserve wild lands in California and throughout the United States, was published in 2005.

As the head of Carnegie Institution, Merriam's administrative duties led to a reduction in his research for the rest of his career.

[9] Merriam was a founding member of the Galton Institute and a cautious political supporter of eugenics.