The highly seasonal river flow, the narrow channel to the ocean, and the large surface area of the water bodies combine to bring about marked seasonal changes in salinity, and the documentation of salinity behaviour has been critical to understanding water exchange. In Peel Inlet the salinity is at a minimum (typically 5 ppt) in late winter and then rises because of the combined effects of ebbing river flow, exchange with the ocean and surface evaporation; eventually the salinity increases beyond that of the ocean (35 ppt), rising to 45 ppt in some years.¹⁰  The salinity reached in late summer is affected by the occurrence of unseasonal summer storms - thunderstorms or tropical cyclones which rarely move as far south as this system. In late summer the rate of increase in salinity is arrested; insolation falls and water exchange begins to dominate the equation. Salinity is depressed when rain falls directly on the estuary, but especially when rivers respond to rainfall as their catchments become saturated. The minimum salinity reached in the basin in winter is related to the volume of river flow.

Harvey Estuary shows similar seasonal changes (Figure 4), but they are more extreme because of the greater distance from the ocean; salinities in summer may reach 52 ppt. ¹⁰  Estuary flushing by river flow is clearly more rapid in winter, when the volume of water entering by flow is estimated at about 5.8 volumes of the estuary.¹  It is estimated that, including tidal and wind forcing, the gross annual flushing rate for the system is about 10.7 volumes. equivalent to a residence time of about 34 days.¹   The factors which affect water exchange through the inlet channel to this system have been detailed elsewhere ¹¹ and have been the subject of modelling exercises. ¹² On one occasion direct  measurements were attempted for exchange during a period of 5 days in winter,¹³ and the results illustrate the complexity of the interactive processes involved. Over the whole exercise there was a net water inflow because of a barometric increase in water level (see above), even though this was a period of river discharge. The salinity at a sampling station in the middle of the channel changed dramatically in response to diurnal tidal excursions and illustrated that water leaving the estuary was not the same as that which had entered the estuary during the previous flood tide; and that water entering the estuary was "new" marine water, not estuary water previously lost from the system. Nutrient concentrations in surface water, especially nitrate, showed dramatic changes with the ebb and flow of the tides. A budget for the 5 days based on these figures  showed massive loss of nitrogen in surface water (23,500 kg), despite a net inflow of water (3.2 x 10^-7) entering from the ocean.

Water lost from the system is swept northwards by prevailing wind induced ocean-water movement.¹³ Marine water entering the system behaves as a front which can he detected in Peel bottom water. Marine water from Peel Inlet penetrates Harvey Estuary and can he detected as density-driven intrusions during periods of low wind speed; the system is mixed vertically during strong wind.  Thus, in Harvey Estuary there are two states; wind-forced with the water column vertically mixed, and calm with the water column stratified. The constant oscillation between the two states ensures that there is always a horizontal density differential along the length of Harvey Estuary to induce density-driven salt wedge intrusions.¹¹