Seagrass plays a crucial role in estuarine and marine environments by influencing various physical, chemical, and biological processes. Seagrass meadows act as a sediment sink by reducing near-bed water velocity as it passes through their leafy canopy structures. This accumulation of sediment within the seagrass rhizosphere, and the ability of seagrass to oxygenate their rhizosphere via radial oxygen loss from roots, means seagrass may profoundly influence early diagenetic processes that drive the sequestration of trace metal contaminants. However, our understanding of trace metal sequestration, mobilisation and overall metal dynamics in seagrass beds is limited. The aim of this study was to investigate how seagrass meadows influence trace metal biogeochemistry. This was achieved by investigating the host phases (e.g., metal oxyhydroxides, sulfides, organic matter) and chemical speciation of trace metals in seagrass rhizospheres compared to nearby sediments without seagrass, in an urbanised sub-tropical estuary. Furthermore, the relationship between trace metal chemistry and sediment depth was investigated along with the relationship between trace metal speciation and seagrass biomass. This study will provide valuable information towards understanding the role of seagrass in estuarine sediment trace metal biogeochemistry.