Naukati Bay is located at , elevation: 207ft[REF] (Section 18, Township 069 South, Range 080 East, Copper River Meridian) between a pair of sheltered bays (Little Naukati Bay and Naukati Bay) on the West coast of Prince of Wales Island in South-East Alaska.
According to the United States Census Bureau, the CDP has a total area of , of which, of it is land and of it (4.95%) is water.