Polychlorinated dibenzo-p-dioxins, dibenzofurans, and dioxin-like polychlorinated biphenyls (hereafter collectively referred to as ‘dioxins’) are persistent organic pollutants that bioaccumulate through aquatic food webs, posing potential exposure-risks through consumption of seafood. Sydney Harbour in eastern Australia is among the most dioxin-contaminated estuaries globally, due to its longstanding industrial legacy. Arcid cockles (Bivalvia: Arcidae) are harvested from estuarine habitats worldwide, yet little is known about dioxin accumulation by this group. This study provides the first published report of dioxin concentrations in Sydney Cockle (Anadara trapezia). Cockles were composited by body size and analysed for 29 dioxin congeners using NATA-accredited high-resolution gas chromatography coupled with high-resolution mass spectrometry. Toxicity equivalency quotients (TEQs) were calculated following World Health Organization guidelines. Dioxin concentrations were significantly higher in cockles from western Sydney Harbour (1.82 ± 0.07 (mean ± SE) pg TEQ g⁻¹) than those from eastern Sydney Harbour (0.74 ± 0.06 pg TEQ g⁻¹). All cockle total dioxin concentrations were below the Australian seafood screening threshold of 6 pg TEQtotal g-wet-weight−1. Cockle congener profiles were dominated by octachlorodibenzo-p-dioxin (OCDD), and PCBs 105 and 118, with higher concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) at the western site. Cockle dioxin profiles did not reflect sediment contamination levels but did approximately represent water column profiles in previous studies. Our study highlights the need for caution when inferring sediment dioxin contamination from bivalve biomonitoring species. Monitoring programs utilising Sydney Cockle could provide a cost-effective means of tracking water column contamination and inform the periodic need for broader seafood sampling in Sydney Harbour.