Systematic water quality research and monitoring has been on-going in Hamilton Harbour since 1987 in response to the Remedial Action Plan (RAP) for this Area of Concern (AOC). Here we present a spatiotemporal analysis of water quality in the harbour and its biological response from 1987 to 2007. Overall nutrient concentrations have decreased by 16 (SRP), 26 (NH_3-Tot) and 36% (TP) in the harbour, chl a concentrations have decreased by 16% and NO_3/2 concentrations have increased by 27%. Hypoxia in the hypolimnion of Hamilton Harbour remains a common occurrence despite improvements in surface water quality conditions. Seasonal patterns in water quality in Hamilton Harbour are mainly driven by biological activity and show typical patterns observed in dimictic nutrient rich lakes. There is systematic spatial variability in water quality in the harbour which is related to the proximity of point and non-point sources; however, there is coherence among all stations sampled and similar temporal trends were observed for all stations. The biological response in the harbour suggests that phosphorus limited algal growth is becoming more prevalent in Hamilton Harbour and the rate of improvements in water quality should accelerate in the near future following further reductions in phosphorus loadings.