The rural water supply systems in the countryside necessitate sustainability and security assessment to ensure long-term and safe water supply to target beneficiaries. The objective of the study is to analyse the hidden threatening factors in water supply system and recommends sustainability and security assessment model. It also predicts the probability of incidents and security degree of the system. The analytic hierarchy process (AHP) was utilized in the decision analysis for water security parameters (Saaty, 1987; Jin-long, 1992; and Li, Li, Wenyan, Lu, 2011). The water supply system constructed and rehabilitated projects under the KALAHI-CIDSS program of the Philippines were the evaluation sites of the study. It sampled about 5,921 water supply systems constructed and installed in 75 municipalities in Eastern Visayas.. The following were the distribution of the sampled water supply systems: 13 Eastern Samar; 13 from Samar; 12 from Northern Samar; 13 from Leyte; 14 from Southern Leyte; and 1 from the Province of Biliran. The water security includes the pipe system network, water resources sites and source covered both quantity and quality, technical and financial capabilities for long term system operation. The study found out that there is a need for continuous water security assessment so that long-term functionality of the water system will be met.