Karatsu Castle, which stands beside Karatsu Bay, is unusual in that the stonework is rises directly out of the water, using the ocean as a natural moat. It is a medium-size castle with the Honmaru (inner bailey) located on top of Mount Manto, the Ni-no-maru (2nd bailey) and the San-no-maru (3rd bailey) in the west, and the outer structures to the south.

The Ni-no-maru secondary bailey contained the palace of the daimyo of Karatsu and the domain’s administrative offices. The innermost bailey would normally contain a donjon; however there is considerable dispute as to whether or not it actually ever did. Records indicate that a stone foundation base existed from at least 1627, but the Tokugawa government never authorized the construction of a donjon tower. The present donjon is a modern reconstruction based on artists assumptions on what a Keichō period (1596–1615) donjon should look like.