Governments in Australia and internationally are experimenting with policy instruments to facilitate the adoption of farming practices with reduced environmental impacts. The Great Barrier Reef (Australia) is one such case, where sustained efforts over 20 years have yielded insufficient progress towards targets to reduce the impacts of agriculture on water quality in downstream marine ecosystems. We present a critical review of policy instruments as implemented in Great Barrier Reef catchments. We catalogue the evolving mix of policy instruments employed in reef programs, and examine evidence of the effectiveness of agricultural extension, financial incentives, and direct regulation of farming practices. There is little robust evidence to assess instrument effectiveness, in part due to the evolving mix of the instruments employed, weak program evaluation and heterogeneity of agricultural enterprises. We identify the need to improve the understanding of instrument fit to landholders and enterprises. We recommend a modelling approach to clarify pathways to impact and guide improved policy evaluation.