Policy makers wanting to increase protection of the Great Barrier Reef from pollutants generated by agriculture need to identify when measures to improve water quality generate benefits to society that outweigh the costs involved. The research reported in this paper makes a key contribution in several key ways. First, it uses the improved science understanding about the links between management changes and reef health to bring together the analysis of costs and benefits of marginal changes, helping to demonstrate the appropriate way of addressing policy questions relating to reef protection. Second, it uses the scientific relationships to frame a choice experiment to value the benefits of improved reef health, with the results of mixed logit (random parameter) models linking improvements explicitly to changes in ‘water quality units’. Third, the research demonstrates how protection values are consistent across a broader population, with some limited evidence of distance effects. Fourth, the information on marginal costs and benefits that are reported provide policy makers with key information to help improve management decisions. The results indicate that while there is potential for water quality improvements to generate net benefits, high cost water quality improvements are generally uneconomic. One implication for policy makers is that cost thresholds for key pollutants should be set to avoid more expensive water quality proposals being selected.