Abstract As much as 60% of the nitrate in water in England is thought to derive from agriculture. Legislation aims to improve water quality by limiting nitrate concentration in surface and groundwaters to 50 mg l −1. The UK Government responded to the requirements of the EC Nitrate Directive by delineating Nitrate Vulnerable Zones (NVZs) to cover 55% of England in 2002 and increased it to 70% in 2009. In this study we assessed the cost-effectiveness of measures for implementation in livestock systems to mitigate nitrate leaching in the UK. These estimates were prepared for a range of hypothetical farms representative of typical dairy, beef and sheep farms at different locations in England and Wales and for a list of mitigation measures identified to reduce leaching. The NGAUGE and NFixCycle models were used to estimate leaching from these systems. The costs of implementation of the mitigation measures were also assessed in order to evaluate the cost-effectiveness of these measures. In general, the most effective measures to reduce leaching for all systems were the ones that involved a reduction in stocking rates and grazing time, followed by those involving improvements in fertiliser and crop management. Only in the case of the dairy system was effectiveness affected by location of the farm. The costs for implementation in the sheep system were relatively low compared with beef and dairy systems. Implementation of some of the measures with high cost-effectiveness would need to be incentivised financially or with legislation due to the high costs involved.