Almost all of the harbour is navigable by sailing vessels with no submerged rocks or navigational hazards except for a small area around Black Swan Island at Old Bay in the harbours north. Of the four main inflows only Melaleuca Creek is truly navigable and maintains a depth in excess of for more than upstream of "Claytons Corner" which provides marine access to Melaleuca. With the exception of the waters around the harbour entrance, most of the harbour has a relatively flat seabed with an average depth of . 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 . The true deepest point in the harbour is where the three channels meet between Platypus Point and Nixon Point which reaches due to the dredging action of the tide.