Heavy flooding and sedimentation pose severe threats to the oyster aquaculture industry in New South Wales, Australia. This study extracted sediment cores and used 210Pb radioisotopes and elemental analysis to examine sedimentation rates and chronologies beneath oyster aquaculture leases, a remnant oyster reef, and mangroves across three NSW estuaries. This study provided the first age estimates for sediment beneath S. glomerata reefs and aquaculture. The oyster aquaculture sediment core that was reliably dated was in a tributary of Port Stephens, while the core beneath the lease in the Nambucca River was mixed, and the core in Gogley’s Lagoon, Camden Haven River, provided a negative SAR, indicating erosion. Oyster reefs and aquaculture in Port Stephens both had high rates of sedimentation at the surface of the sediment core, while sediment collected from oyster reefs was older (1939 vs. 1976) and had higher concentrations of nutrients (C, N, P) and heavy metals associated with human activities (As, Cu, Pb) than oyster aquaculture. Sediment beneath mangroves upstream of oyster aquaculture in the Nambucca River was dated to 1943, with nutrient and metal enrichment peaks coinciding with a heavy flood event in 2012. Mangrove sediments in Gogley’s Lagoon, Camden Haven River, were dated to 1987 and had the lowest nutrient concentrations of the estuaries examined in this study. This study confirms that sedimentation patterns in highly dynamic environments around oyster leases are likely influenced by estuarine morphology, extreme weather events, and habitat-forming species.