The behaviour of iron and manganese in the Yarra estuary (a rather small, well-stratified estuary) is shown to be closely linked with the magnitude of the Yarra River inflow. When river flows are average to high, the filterable metals are present largely in bound or non-ion- exchangeable forms (iron > 90%, manganese 70-80%). Filterable iron levels in surface water from the estuary decreased with increasing salinity, and the filterable manganese levels firstly increased in the upper, low-salinity region of the estuary and then decreased with increasing salinity. Possible reasons for these changes are discussed. When low river flows existed, the concentration of filterable iron and manganese both increased markedly in the bottom, saline water of the estuary. Mixing of small amounts of these enriched bottom waters with outflowing surface waters resulted in the concentrations of filterable metal in surface water increasing with increasing salinity.