Conceptual models of circulation theorise that the dominant forces controlling estuarine circulation are freshwater discharge from the riverine section (landward), tidal forcing from the ocean boundary, and gravitational circulation resulting from along-estuary gradients in density. In micro-tidal estuaries, sub-tidal water level changes (classified as those with periods between 3 and 10 days) with amplitudes comparable to the spring tidal range can significantly influence the circulation and distribution of water properties. Field measurements obtained from the Swan River Estuary, a diurnal, micro-tidal estuary in south-western Australia, indicated that sub-tidal water level changes at the ocean boundary were predominantly from remotely forced continental shelf waves (CSWs). The sub-tidal water levels had maximum amplitudes of 0.8 m. were comparable to the maximum tidal range of 0.6 m, propagated into the estuary to its tidal limit, and modified water levels in the whole estuary over several days. These oscillations dominated the circulation and distribution of water properties in the estuary through changing the salt wedge location and increasing the bottom water salinity by 7 units over 3 days. The observed salt wedge excursion forced by CSW was up to 5 km, whereas the maximum tidal excursion was 1.2 km. The response of the residual currents and the salinity distribution lagged behind the water level changes by similar to 24 h. It was proposed that the sub-tidal forcing at the ocean boundary, which changed the circulation, salinity, and dissolved oxygen in the upper estuary, was due to a combination of two processes: (1) a gravity current generated by a process similar to a lock exchange mechanism and (2) amplified along-estuary density gradients in the upper estuary, which enhanced the gravitational circulation in the estuary. The salt intrusions under the sub-tidal forcing caused the rapid movement of anoxic water upstream, with significant implications for water quality and estuarine health. (C) 2007 Elsevier Ltd. All rights reserved.