The seasonal closure of tidal inlets is a common feature in microtidal, wave dominated regions where streamflows and/or longshore sediment transport are highly seasonal. This closure of the inlet obstructs navigation and deteriorates the flushing mechanism of the estuary/lagoon connected to the inlet, which could result in a degradation of the water quality. This paper presents results of a numerical study undertaken at Wilson Inlet, which is a seasonally open tidal inlet situated along the south western coast of Australia. The objectives of the study were to determine the dominant processes that govern the flushing rate (i.e. tidal exchange, wind, streamflow etc.), to test the response of the flushing characteristics of the estuary to different management options and to obtain a quantitative and qualitative estimate of the flushing rate of the estuary under different conditions. The results of the study indicate that streamflow is the major influence governing the flushing of the estuary while tidal exchange, wind and entrance channel location have a minimal effect. Regions of high residence times (low flushing rates) exist along the eastern and southern boundaries of the estuary. Under high streamflow conditions sea water does not propagate into the deeper parts of the estuary as the intrusion that forces into the estuary during flood periods is flushed out by the following ebb period. However, when the streamflow is less than the mean annual streamflow seawater propagates into the deeper parts of the estuary and is not flushed out by the ebbing tides.