Agriculture has a substantial impact on the quality and quantity of groundwater. The excessive usage of nitrogen fertilizers and manure on agricultural lands can increase the nitrate concentrations in surface water and groundwater. Over the past 150 years, the catchments adjacent to the Great Barrier Reef (GBR), Australia, the world’s largest coral reef ecosystem, have been drastically changed with the development of the catchments for farming activities. Therefore, there is potential for nutrients (carbon, nitrogen and phosphorus) to be discharged beneath the plant root zone to the vadose zone, then to groundwater or be transported in runoff from sugarcane fields and eventually into creeks and rivers that feed into the GBR. This paper has investigated the fate of nutrients that leach through the vadose zone under a sugarcane field in the South Johnstone catchment, in the Wet Tropics. Using a real time monitoring technique, the vadose zone monitoring system (VMS), the temporal and spatial distribution of nutrients in the vadose zone has been studied. NOx-N concentrations in leachate under sugarcane varied over time at different depths. Generally, the concentration of Nitrate decreased over time but increased with depths. Ammonia was found to range from 0.01 to 0.49 mg/L, showing a difference between samples collected before and after fertilization in 2016 -2018. Total Organic Carbon (TOC) losses in the vadose zone also varied with time. Phosphate in the vadose zone was found below the detection limit, demonstrating plant uptake and hereafter the phosphate attenuation in the soil. The processes affecting the transport of nutrients through the vadose zone and time lags that occur before these contaminants reach ground water have also been determined.