Coconut is naturally sealed with coconut water inside. Microbial contamination occurs only after the seal is broken during extraction. This study evaluated changes in the microbiological, physicochemical, and chemical properties of coconut water during postharvest storage at ambient and refrigerated temperatures. Initial microbial counts ranged from 2 to 5 log CFU/mL, while physicochemical factors, including total soluble solids (TSSs), pH, and sugar content (4–7 °Brix, 5.0–5.5, 4–6% g/100 mL), were consistent. The dynamic changes in the physicochemical properties of coconut water stored under both conditions exhibited a clear correlation with the increased microbial populations. Fructose was the primary sugar, with citric and malic acids as major acids, while the predominant volatile compounds were ethanol, ethyl acetate, ethyl ester, acetic acid and octanoic acid. Storage conditions led to similar microbial and physicochemical changes, but ambient temperature accelerated spoilage 10 times faster than refrigeration. Sucrose decreased steadily, whereas fructose and glucose remained stable until a precipitous decline coincided with lactic acid bacteria (LAB) reaching >6 log CFU/mL on the final day of storage. Weissella cibaria and Leuconostoc spp. are the main species in coconut water. The presence of specific volatile compounds, including octanoic acid, acetic acid, ethyl acetate, and butyl phenol, is associated with the activities of Lactobacillus, particularly Weissella. There was a clear relationship among microbial groups and populations, total titratable acidity (TTA), and sensory criteria. Remarkably, TTA was closely correlated with total plate count (TPC) (>5 log CFU/mL) and an unacceptable sensory rating.