This paper describes the design and implementation of a choice experiment to understand Aucklanders’ preferences for environmental qualities associated with the effects of urban run-off on marine coastal environments. Auckland’s coastal environments are affected by a range of ecological and human factors. While much research has been undertaken in the area of ecology, little is understood of human preferences for coastal environments and their management. An unlabelled choice experiment was developed with three environmental quality attributes specified at three broad coastal categories. The environmental qualities are ecological health, water clarity, and underfoot conditions. Willingness to pay estimates for these attributes indicates that respondents show a strong preference for improved environmental quality at outer coastal beach locations over middle and upper harbour locations. Water quality leads ecological health, then underfoot conditions in importance at beach locations. An application is discussed in which a hypothetical project consisting of policy and engineering components delivers changes in water quality and underfoot conditions in the Auckland upper harbour areas. A 95% confidence estimate of the money value of that change ranges from $ 783 m. to $ 1,122 b. The key outcome is demonstration of the choice experiment as a statistically robust and flexible approach to making sense of Aucklanders’ complex preferences for coastal ecosystem management.