The Cabadbaran River Irrigation System (CabRIS) supports about 3,212 hectares of farmland for irrigation. Unfortunately, the local irrigation office reported that only a small percentage of its entire service area was irrigated during the past cropping seasons. The water yield has been dwindling; hence an irrigation system management plan will address the water resource crisis. As a project component, the team carried out a floristic assessment for the entire watershed. The study used the quadrat-transect sampling method to assess and characterize the structure and species composition of the riparian areas of the main Cabadbaran River, Cabadbaran City, Agusan del Norte, Philippines. Results recorded about 109 morpho-species belonging to 46 families and 88 genera from the sampling sites. Nineteen species were listed either on the Philippine Red List and or on the IUCN Red List of Threatened Species. The result of the plant diversity assessment revealed that biodiversity in riparian forests in the watershed was low to very low due to the massive rampant disturbance in the area. The riparian ecosystem of the Cabadbaran River represents a fragile ecosystem that is threatened by increasing demands on the regional water supply and the conversion of lands into tree plantations and agriculture. Addressing these driving forces causing biodiversity loss will impart a significant challenge for irrigation and land managers in the region.