Four fishery important species were tracked in a permanently-open estuary on the south-coast of Western Australia, the Walpole-Nornalup Estuary, to quantify and compare their residency within the system and responses to various environmental drivers. Twenty three Black Bream (Acanthopagrus butcheri), 21 Southern Bluespotted Flathead (Platycephalus speculator), 10 Snapper (Chrysophrys auratus) and 10 Tarwhine (Rhabdosargus sarba) were implanted with internal acoustic transmitters between July 2014 and February 2016 and monitored using a fixed acoustic array for a period of up to 656 days. Marked differences in movement patterns, habitat preferences and spatial area use of the system were detected among species and between seasons of the year. Acanthopagrus butcheri were highly mobile and used vast areas of the system from the estuary mouth to the upstream extent of estuarine affinities. While two other sparids, C. auratus and R. sarba, were also highly mobile, their movements were largely confined to the marine-influenced middle and lower estuary, and more than half of individuals tagged left the system, with only the latter species displaying return movements. Comparatively, individuals of P. speculator exhibited far higher site attachment and typically remained near their release sites within the estuary, although five fish undertook rapid one-way migrations out of the estuary. These results enhance existing knowledge of how these important species use estuaries and highlight areas where populations are potentially most vulnerable to fishing pressures.