Freshwater ecosystems, such as wetlands, are among the most impacted by agricultural expansion and intensification through extensive drainage and pollution. There is a pressing need to identify ways of managing agricultural landscapes to ensure food and water security without jeopardising biodiversity and other environmental benefits. Here we examine the potential fish biodiversity and landholder financial benefits arising from the integration of constructed lagoons to improve drainage, flow regulation and habitat connectivity within a sugarcane dominated catchment in north Queensland, Australia. A hybrid approach was used, combining the findings of both fish ecological surveys and a financial cost-benefit analysis. We found that the constructed lagoons supported at least 36 native freshwater fishes (over half of all native freshwater fishes in the region), owing to their depth, vegetated margins, moderate water quality and high connectivity to the Tully River. In addition to biodiversity benefits, we estimated that surrounding sugarcane farms would have financially benefited from reduced flooding of cropland and the elevation of low-lying cropland with deposited spoil excavated from lagoon construction. Improved drainage and flow regulation allowed for improvement in sugarcane yield and elevated land increased gross margins from extending the length of the cane production cycle or enabling a switch from cattle grazing to cane production. Restoring or creating wetlands to reduce flooding in flood-prone catchments is a globally applicable model that could improve both agricultural productivity and aquatic biodiversity, while potentially increasing farm income by attracting payments for provision of ecosystem services.