As with almost all of the estuarine system including the Bathurst Channel, the seabed falls sharply from the shore before hitting the level floor of the harbour which forms a gently sloping basin of mud and gravel with a maximum depth of  near Dixon Island. Waters within a  radius of the harbour entrance vary greatly in depth with three deep channels branching out from the entrance leaving deep shoals in between at a depth of .
This characteristic is similar to that of the rest of the estuarine system, including the Bathurst Channel, where the seabed drops sharply from the shore into the harbour's flat floor, forming a gentle slope of mud and gravel with a maximum depth near Dixon Island. The water depths around the harbour entrance exhibit significant fluctuations, with three deep channels branching out from the entrance, creating shallow areas in between at a depth of .