Sydney Harbour is one of Australia’s most heavily recreationally-fished estuaries, but despite ongoing improvements to estuary health the ghost of industry-past haunts the fishery through organic contaminants in sediments and biota. Dioxins (polychlorinated dibenzo-p-dioxins and furans [PCDD/Fs] and dioxin-like polychlorinated biphenyls [dl-PCBs]) are one of the most significant of these contaminants, and areas of sediment in Sydney Harbour have been shown to carry some of the highest levels of dioxin contamination in the world. We present a synopsis of the dioxin contamination issue in Sydney Harbour, and examine the impacts of partial removal of contaminated sediments in Homebush Bay, a decade after remediation occurred. Dioxin concentrations and congener profiles differed substantially among species, zones and times, with lower concentrations in crustaceans post-remediation, but no such pattern in fish. The findings are discussed in the context of species biology and ecology, and patterns related to recent modelling of recreational fishing effort across the estuary. We conclude by highlighting the implications for the fishery into the future.