To achieve water quality targets, management practice change in the sugar cane industry has been a large focus for natural resource management initiatives such as Reef Plan and Reef Rescue. Considerable public funds have been targeted at landholders to change on-ground management practices. However, the economic implications for landholders are not well understood. To further inform future policy development of the upcoming Reef Water Quality Protection Plan 3 and Reef Rescue 2, the economic costs and benefits to landholders are required. This research used a case study approach to consider the economic implications of improved soil management through an extended fallow period in the Mackay-Whitsunday region. The results demonstrate the complexity of creating effective policy design for adoption of improved management practices for water quality in a semi perennial farming system.