National irrigation systems (NIS) are crucial to the Philippine agriculture sector. Currently, they account to about half of the area that supply rice in the country, making their operation and maintenance critical in the food sufficiency program of the government. Despite the huge budget allocated to the National Irrigation Administration (NIA), however, many NIS are underperforming based on selected indicators. For instance, this study finds that NIS are still suffering from various issues, such as siltation, flooding, deterioration of canals, and other institutional and policy issues. Some of the NIS also experience salinity problems, which can pose serious effects on crop production and yield. To address these issues, the study urges the government to adopt good watershed management and enhance maintenance and rehabilitation of NIS facilities, including pipe network. It also calls for the regular monitoring and proper implementation of policies related to illegal activities that affect irrigation system functionality, such as those relating to illegal settlers, pumping, and waste disposal.