Fresh and aged coconut water (CW) samples were introduced directly into the electrospray ionisation (ESI) source, and were combined with the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) technique to characterise in situ chemical compounds produced during natural ageing (from 0 to 15 days) at room temperature (23 °C). The ESI-FT-ICR MS readings were acquired and the data were correlated to conventional methodologies: pH, total titratable acidity (TA), total soluble solids, microbial analyses, and ultraviolet visibility (UV–vis) spectroscopy analysis. In general, the pH and TA values changed after 3 days of storage making the CW unsuitable for consumption. The ESI(−)-FT-ICR data also showed a clear and evident change in the chemical profile of CW after 3 days of ageing in the m/z 150–250 and 350–450 regions. Initially, the relative intensity of the natural markers (the m/z 215 and 377 ions–sugar molecules) decreases as a function of ageing time, with the last marker disappearing after 3 days of ageing. New chemical species were then identified such as: citric (m/z 191), galacturonic (m/z 193), gluconic (m/z 195), and saccharic (m/z 209) acids. ESI(−)-FT-ICR MS is a powerful tool to predict the physicochemical properties of CW, such as the pH and TA, where species such as fructose, glucose, sucrose, and gluconic acid can be used as natural markers to monitor the quality of the fruits.