Perchlorate and chlorate are inevitable components in rocket propellants, fireworks, water treatment, bleaching, textile industry, etc. Knowingly or unknowingly, wide use of these chemicals contaminates drinking water systems. The present study assessed the perchlorate and chlorate contamination of bottled water and other drinking well, tap, bore well, rainwater sources of Kerala and other parts of Peninsular India. Other drinking water samples were collected during the pre-monsoon, monsoon and post-monsoon from the 14 districts of Kerala and were analyzed for perchlorate and chlorate using liquid chromatography-mass spectrometry. Most of the locally available brands of bottled water were found to be contaminated with perchlorate and chlorate. Mean value of perchlorate was found to be 93.19 ppb, and that of chlorate was 3692.07 ppb, both exceeding the health reference level. The continuous consumption of water with high level of perchlorate content can cause high risk, and the probability of increasing thyroid disorders is high. Perchlorate was detected from well, tap and bore well water samples, and the maximum perchlorate was observed for the premonsoon season, whereas the minimum noticed in the monsoon samples. The high concentration of perchlorate detected in groundwater was mainly due to the industrial units and firework manufacturing and display sites.