Mitigating nitrogen leaching from agricultural land is imperative for enhancing the ecological status of aquatic ecosystems. Incorporating the knowledge and perceptions of farmers regarding the feasibility and effectiveness of implementing nitrogen reduction measures is vital for increasing the adoption rate of such measures and related policies. Concurrently, the insights and perspectives of scientists advising policymakers on the implementation of these measures can facilitate a more comprehensive understanding of the barriers and potential for implementation. In this study, we employ Q methodology to elucidate the opinions of 11 farmers and 14 key scientists involved in providing contractual science policy advice to Danish ministries on nitrogen reduction measures. Results show that across the perspectives of farmers and scientists, four main factors (viewpoints) can be identified: ‘Evidence-driven viewpoints’, ‘On-farm efficiency-driven viewpoints’, ‘Hydrological and landscape-scale viewpoints’, ‘Innovation-based viewpoints. From this, we suggest that within the field of nitrogen mitigation and implementation, there is a general broad division and opposing perspectives between scientists and farmers. The evidence presented here shows that scientists’ viewpoints do not correspond to the viewpoints of farmers in most cases. Scientists broadly believe that landscape and long-term measures, especially wetlands, are most effective nitrogen measures, according to scientific evidence. This clashes severely with some farmer participants, who strongly believe that there should be more personal freedom and flexibility to make individual farm level management choices. This is a significant barrier to the uptake of the best possible measures.