Cocos Lagoon appears as a small incomplete coral atoll attached to the south-western coast of Guam near the area of the village of Malesso'.

Cocos Island and Babe Island sit atop the southern portion of the Merizo Barrier Reef and separate Cocos Lagoon from the open ocean in the south.

In the north-west, Mamaon Channel separates Cocos Lagoon from the main island of Guam and allows boat access to Merizo.

Southeastward of the channel, down to Achang Bay, there is no separation to the main island of Guam.

Along the west side, the barrier reef uncovers in spots but has no islands.