Much of the bay is shallow. Since the bay is an estuary, it has fresh water, salt water and brackish water. Brackish water has three salinity zones — oligohaline, mesohaline, and polyhaline. The fresh water zone runs from the mouth of the Great River to the village of Gustanuu in the north.
The Gugnulaan Bay is home to numerous fauna that either migrate to the bay at some point during the year or live there year round. There are over 300 species of fish and numerous shellfish and crab species.