The future of the Hurunui River and its catchment has been hotly contested between those who seek to store and/or divert water from the river in order to increase agricultural production and those who would like to see the river undeveloped and the quality of natural resources in the river and catchment improved. The Canterbury Regional Council wished to develop an approach to manage catchment nutrient loads across the region in order to achieve the objectives of its Natural Resources Regional Plan (NRRP) for water quality and aquatic habitats. Our approach, combining stakeholder consultation with choice analysis, was developed and tested in the Hurunui catchment in 2010-2011. The policy objective of the choice experiment was to describe and quantify the preferences of Canterbury Region residents with respect to existing conditions (the status quo) and potential future land use and water quality scenarios for the catchment. It was envisaged that this quantitative information on preferences across the region would be used by policy makers at the same time as they considered the outcomes of the stakeholder deliberative process. At the conclusion of the consultation process there was ‘general acceptance’ of a future development strategy for the Hurunui catchment that would maintain water quality in the main river at 2005-2009 levels while improving the tributaries to 1990-1995 water quality. Results from the choice experiment are broadly supportive of this approach. Canterbury region residents would require substantial compensation (mean $244-$315 per household per year) before they would accept a decline in water quality in the main river or in the tributaries. Willingness to pay for improvements in the main river is lower with a mean of $25-$33 per house hold per year.