Sydney estuary (Australia) catchment is substantially urbanised (80%) and small (480 km2) with a large population (2.5 million) and is therefore highly sensitive to anthropogenic influence. The Model for Urban Stormwater Improvement Conceptualisation used to model nutrient export to the estuary determined an average annual load of 475 t total nitrogen, 63.5 t total phosphorus and 343,000 t total suspended solids. Model verification included intense, short-term water sampling and analysis undertaken in the current project and use of published data spanning 10 years. Under high-rainfall conditions (>50 mm day(-1)), the estuary becomes stratified and nutrients are either removed from the estuary directly in a plume or indirectly by advective/dispersive remobilisation. The majority of the nutrient load is delivered during moderate rainfall (5-50 mm day(-1)) conditions and accumulates close to discharge points and remains in the estuary. To significantly reduce nutrient load, management strategies should aim to minimise low and moderate rainfall pollutant loads.