There is a need for innovative and cost-effective approaches to deliver further water quality improvement and ecosystem protection in Great Barrier Reef catchments. Transitioning low-lying, marginal sugarcane to alternative land-uses that require lower or no nitrogen inputs, but still provide farmers with income streams, is an attractive solution. Here, a multi-criteria analysis was conducted to identify sites suitable for such alternative land-uses. The cost-effectiveness of DIN reductions from these land use changes were calculated, accounting for reductions in annuity gross margins and land conversion cost. In certain locations (where conversion costs are low and DIN decreases are high) treatment wetlands and no-input grazing offer cost-effective DIN reduction in the range of 20–26$/kg DIN. This compares favourably with existing agricultural extension-based approaches (c. $50/kg DIN reduction). Ecosystem service wetlands (i.e., restoration for fish production) – again when appropriately situated offer the prospect of even more cost-effective performance (11–14 $/kg DIN reduction). These results, in conjunction with best management practices, support the premise that alternative land-uses are cost-effective options for improving water quality in certain areas of low-lying, low productivity sugarcane land. On-going investments by government bundled with private market funding could be appropriate for supporting such land use transitions.