Bangor Annex, is located on the eastern shore of Hood Canal near the town of Silverdale. Hood Canal has several internal bays, the largest of which is . Most of Dabob Bay is a Naval Restricted Area, and is used by the submarines stationed at the Bangor Base. Quilcene Bay is an inlet extending northwest from Dabob Bay. Near the north end of Hood Canal is Port Gamble, a bay and a town of the same name.

Several rivers flow into Hood Canal,