Nathaniel Bowen (June 29, 1779 – August 25, 1839) was the third bishop of South Carolina in the Episcopal Church in the United States of America.

The family moved to South Carolina when Nathaniel was young and his father died soon after.

Bowen graduated from the College of Charleston in 1794; was ordained deacon on June 3, 1800, and priest in October 1802.

He was consecrated bishop of South Carolina on October 8, 1818, serving until his death in Charleston on August 25, 1839.

Nathaniel Bowen was the 17th bishop consecrated for the Episcopal Church.