The Kakanui River and estuary in the Northern Otago Province in southern New Zealand has long been a popular recreational area for both residents and tourists. However, long-term surface water quality monitoring has shown an increase in nutrients in both the river and estuary which has caused growth of macro-algae and reduced recreational use. Otago Regional Council has set a nitrogen target for the Kakanui River of 0.075 mg/L. It has also set a nitrogen leaching rate of 20 kgN/ha/yr over the adjacent Kakanui-Kauru Alluvium aquifer, which is a thin gravel aquifer highly connected to the Kakanui River. In a bid to understand the groundwater-surface water interaction with respect to nitrate losses and effects on the Kakanui River, a monitoring program is being carried out. Fifteen monitoring bores and 14 surface water quality and/or flow sites have been monitored on a fortnightly / monthly basis from March 2014 to March 2017. An Estuary Hydrodynamic Model was completed to determine an appropriate instream nitrogen target. The program is on-going, but results to date verified the 0.075 mg/L nitrogen concentration was appropriate to stop prolific algae growth. Groundwater modelling will be carried out in 2017/18 to verify if the nitrogen leaching rate (20 kgN/ha/y) is appropriate to deliver nitrogen target of 0.075 mg/L in the Kakanui River. Preliminary results show that in a dynamic system it is not possible to manage different water sources on their own (estuary, river or aquifer). An integrated approach is required to solve the water quality issues. Depending upon the modelling results there may be implications for land use management to meet community values. Strategic planning between science and policy will be required to provide the best outcome for both the community and the environment.