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Shellfish reefs have been lost from bays and estuaries globally, including in the Swan-Canning Estuary in Western Australia. As part of a national program to restore the ecosystem services that such reefs once provided and return this habitat from near extinction, the mussel Mytilus galloprovincialis was selected for a large-scale shellfish reef construction project in this estuary. To assess the potential filtration capacity of the reef, estuary seston quality, mussel feeding behavior, and valve gape activity were quantified in the laboratory and field during winter and summer. In general, estuary water contained high total particulate concentrations (7.9–8.7 mg L−1). Standard clearance rates were greater in winter (1.9 L h−1; 17 °C) than in summer (1.3 L h−1; 25 °C), the latter producing extremely low absorption efficiencies (37%). Mussel valves remained open ~97% and ~50% of the time in winter and summer, respectively. They often displayed erratic behavior in summer, possibly due to elevated temperatures and the toxic microalgae Alexandrium spp. Despite numerous stressors, the reef, at capacity, was estimated to filter 35% of the total volume of the estuary over winter, incorporating 42.7 t of organic matter into mussel tissue. The reefs would thus make a substantial contribution to improving estuary water quality.