Context Agricultural land use is intensifying globally. Irrigation and other farm practices associated with intensification, such as cultivation, grazing, and fertiliser application, can increase nutrient losses. Variable rate irrigation (VRI) systems manage irrigation to spatially variable soils and different crops (zones). We lack knowledge on nutrient losses under zone-specific irrigation for mixed-cropping systems (combined crop and livestock grazing). Aims This study evaluated drainage, nitrogen, and phosphorus leaching losses under zone-specific irrigation for a temperate mixed-cropping system. Methods The study site had sheep grazing and crops including peas, beans, wheat, turnips, plantain, and ryegrass-white clover pasture. It had a variable-rate centre-pivot irrigator for two soil zones (free draining Zone 1; poorly drained Zone 2). Drainage flux meters (DFMs) collected drainage leachate, and samples for measurement of nitrogen (N) and phosphorus (P) concentrations. Soil water balance data and statistical modelling evaluated nutrient leaching losses over 5 years. Key results The mean leaching load of NOx-N (nitrate + nitrite) across 5 years was 133 (s.d. 77) and 121 (s.d. 97) kg N/ha/year for Zone 1 and Zone 2, respectively. Similarly, the mean leaching load of reactive P across all years was 0.17 (s.d. 0.30) and 0.14 (s.d. 0.14) kg P/ha/year for Zone 1 and Zone 2, respectively. The nitrogen concentrations and loads generally had greater uncertainty in Zone 2. Conclusions The DFMs worked well for the free draining sandy soil. However, fewer samples were collected in the silt soil, requiring the statistical modelling developed in this study. This study gave a reasonable estimate of annual leaching load means, but the indicators of their within-year variation were not reliable, partly due to differences in sampling frequency. With some exceptions, there was generally more NOx-N leaching from the free draining Zone 1. VRI provided a system to control irrigation-related drainage and leaching in these soil zones. Implications Drainage flux meters are more reliable in well-drained than in poorly drained soil. Given the lack of published studies, this study has improved knowledge of nutrient losses under zone-specific irrigated mixed-cropping systems in a temperate climate.