Agriculture activities in coastal catchments often contribute pollutant runoff such as nitrogen (N), phosphorus (P), and trace metals to estuarine environments. Here, we determine the historical impacts from agricultural expansion using sediment samples from an estuary and a coastal wetland downstream from intensive historical banana, and now, blueberry plantations (Hearnes Lake estuary, NSW, Australia). The three 210Pb dated sediment cores and surface sediment samples analyzed in this study revealed that trace metals (As, Cd, Cu, Pb, Zn, Cr) and N fluxes recently increased as a result of increasing sedimentation rates. Several moderate localized enrichments were observed in recent sediment layers. Most importantly, we found a clear link between the sediment P profile and recent blueberry cultivation. P enrichment increased by 9-fold and sediment fluxes by over 40-fold (up to 12.6 mg m−2 year−1) during the expansion of blueberry cultivation within the catchment since 2002. The trapping of sediments enriched in P by the wetlands provided a good chronology of agricultural practices in the region. With a global and regional increase in estuarine eutrophication, this study further demonstrates the importance of agricultural sources and the role coastal wetlands play in sequestering P from runoff.