The Subak is a traditional Balinese irrigation and farming management system rooted in socio-religious customs and ecological harmony. The sustainability of the Subak, however, is increasingly threatened by contamination from domestic, livestock, and small-scale industrial waste. This study assessed the types, sources, and practices of waste management in Penebel District in Bali with a participatory mapping approach involving surveys, field observations, and focus group discussions with farmers and local officials. Findings from 38 Subak irrigation systems revealed that 52.63% of the Subak areas were primarily affected by domestic waste while 21.05% faced mixed contamination from domestic and livestock waste. Among all, the predominant waste types included 44.74% of organic materials, such as manure and agricultural residues, and 34.21% of inorganic materials like plastics and packaging. Alarmingly, 57.89% of the Subaks left waste untreated in irrigation channels whereas 41.1% of the households disposed waste directly into drainage or irrigation ditches. Only a small portion, 21.06%, practiced composting. These informal waste practices were exacerbated by limited institutional support and deteriorated irrigation infrastructure, as 28.95% of the Subak irrigation channels were in damaged condition. In this connection, this study also shed light on the imperative for differentiated and community-based waste management strategies, aligned with the principles of organic farming. Recommended interventions included organic waste composting, structured inorganic waste collection, Awig-Awig revitalization, and environmental education to change local behaviors. The integration of participatory mapping with environmental assessment provided a practical and culturally relevant tool for empowering the Subak communities with sustainable waste and water management. Protecting the Subak landscape from waste is indispensable for safeguarding both agricultural productivity and unique cultural heritage in Bali.