Although it often has a constricted tidal mouth, it is nearly always open, only occasionally closing for short periods. The upper estuary is at times poorly flushed, stratified, and susceptible to phytoplankton blooms. Mouth constriction, reclamation, and causeways in the lower reaches of the estuary have contributed to the central estuary becoming dominated by muddy sediments in poor condition.
The estuary supports a variety of substrate types, extensive areas of salt marsh, but no seagrass. It is muddy, with a high level of eutrophication , extensive gross eutrophic zones, soft muds, poor sediment oxygenation, and high phytoplankton concentrations. However, there are no nuisance macroalgal growths present.
Historically, there has been habitat change and loss of estuary salt marsh (estimated at ~100ha overall) and the 200m terrestrial buffer is now dominated by a mix of industrial activities, roading, and grassland. The most degraded conditions are in the relatively sheltered central basin of the estuary, with the lower estuary being well flushed with more mobile sands due to a stronger tidal influence and wave action during storms.
