Releases of excess nitrogen and phosphorus from fertilisers applied in agricultural production cause eutrophication in the aquatic ecosystem. This study assessed the marine and freshwater eutrophication potentials associated with the fertiliser application in rice, maize, cassava, sugar cane and oil palm, cultivation in Thailand using a life cycle assessment characterisation model at midpoint and endpoint levels. The total marine eutrophication potential was 209,632,298 kg N eq while the total freshwater eutrophication potential was 2,044,136 kg PO4 eq. The associated ecosystem damage was 2,643,706,874 PDF.m2.year. Marine eutrophication potential was the major contributor to the ecosystem damage, accounting for 99.1% of the total. Sugarcane cultivation was the main contributor (28.5%) to eutrophication impacts, followed by rice (28.0%), cassava (16.0%), oil palm (14.8%) and maize (12.7%). Nitrate was the major contributor to marine eutrophication (92.7%), far more than ammonia (6.7%) and nitrogen oxide (0.6%). Seventeen scenarios were developed and analysed in view of mitigating the ecosystem damage through emission reduction. Applications of a nitrification inhibitor (Dicyandiamide) with fertilisers, 4R nutrient management practices (right source, right rate, right time and right place) and the integrated scenario of these two scenarios depicted substantial decreases in ecosystem damage by 46%, 40% and 68%, respectively compared to the damage from existing fertiliser application rates. Therefore, the integrated approach would be recommended as the most effective way to reduce the eutrophication impacts from fertilisers. Existing studies have significantly focused on ammonia mitigation with less attention on nitrate reduction. This assessment revealed that nitrate reduction plays a crucial role in reducing the eutrophication impacts and new policy focuses should include the nitrate reduction. Future studies could consider threshold values for the impacts of freshwater and marine eutrophication to discover the risk level of eutrophication.