 In recent years, agriculture has emerged as the largest contributor to the environment that exists in itself. It is responsible for 70% of fresh water uses, over 30% of greenhouse gas emissions, and is one of the leading cause of climate change. Agriculture has been identified as the major source of soil and water pollution, mainly through fertilizer and freshness among many other fields. The cultivation in Sri Lanka is either rain-pelo irrigated. Misirrigation systems operate at different scales, mainly utilising surface water. The irrigation systems in the rice, the paddy land state is acting as a cluster. The drainage water coming from the upstream paddy fields are utilised by the immediate downstream paddy fields. The research aims to understand the spatial and temporal variation of the Dhadruwa basin, the fourth largest river basin in Sri Lanka. What samples from various locations of the basin were collected over an year and analysed for pesticides, heavy metals and other agricultural pollutants. Load policies for a crop in an agricultural system can lead to environmental or human health risks. This research develops a framework that informs decision makers about cross-sectional policy solutions. Although food security is critical for all countries, reducing water pollution is equally important to protect environmental health that maintains various ecosystem functions contributed to food security.