Four primary habitats have been identified in the St Lucia estuarine system, each having a suite of characteristic vegetation types. These can be described as follows: (1) open water; (2) intertidal shoreline; (3) 'dry' shoreline and island (i.e. those habitats without any freshwater source other than rainfall); and (4) groundwater-dependent shoreline. The responses of these habitats to changes in water level, salinity and other determinants have been described. An understanding of these responses facilitates the management of the estuary mouth. Past records indicate that the mouth closed naturally at the start of a drought, but the management policy was to keep it open by dredging the berm which developed at the mouth. While the mouth was open, seawater replaced estuary water lost to evaporation and the system eventually became hypersaline. An assessment of the range of physical conditions that occur in St Lucia Estuary and the response in each habitat indicated that the open mouth hypersaline condition is the most detrimental, resulting in die-back of shoreline vegetation. This understanding supported the management decision that resulted in the mouth being kept closed since 2002. Since then, the estuary has been characterised by high salinity but low water levels, and therefore large-scale die-back of shoreline vegetation has not occurred.