Filter feeding bivalves are useful bioindicators for the detection of biologically available pollutants. We investigated trace metals, metalloids, and pesticides in leaf oyster (Isognomon ephippium) soft tissue and shells and compared them to sediment in five estuaries in northern New South Wales, Australia. Concentrations of Pb, Cr, Mn, Ni, Fe and Al were higher in sediments, whereas Zn, Cd, Ag, Hg, Se and As bioaccumulated in the soft tissue. The amount of Cu, Hg and Ni in the sediment from Tweed and Richmond River estuaries exceeded the Australian national sediment quality guideline values. Only one pesticide, atrazine, was detected in leaf oyster soft tissue. Combinations of six elements in the soft tissue were the best predictors of oyster condition index and shell size, whereas sediment contaminants showed weak relationships. Overall, the bioaccumulation of metals and metalloids increases with leaf oyster size and reduces leaf oyster condition, suggesting these large bivalves are useful bioindicators for pollution in estuarine environments.