Water kefir is a non-dairy fermented beverage whose flavor arises from complex interactions among lactic acid bacteria, yeasts, and their metabolites. The volatile and metabolic profiles of water kefir fermented with unrefined brown sugar alone, without fruit adjuncts, remain poorly characterized. Here, water kefir was fermented for 72 h in a simplified unrefined brown sugar-only medium, and volatile organic compounds (VOCs) and metabolites were analyzed using gas chromatography-ion mobility spectrometry (GC-IMS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS)-based untargeted metabolomics. Twenty-six VOC signals (corresponding to 25 unique compounds) were identified, dominated by esters (8), aldehydes (5), and alcohols (4). Two distinct fermentation phases were revealed: an early stage (0–48 h) of rapid ester accumulation associated with shifts in starch, sucrose, and amino acid metabolism, and a late stage (48–72 h) marked by declining ester levels and increased metabolite co-variation network density. Under the investigated conditions, these temporal dynamics suggest that 48 h represents a candidate time point associated with an ester-rich volatile profile, whereas extending fermentation to 72 h yields a more acidic, organic acid- and amino acid-remodeled matrix. Overall, this study provides a preliminary chemical reference for brown sugar water kefir fermentation, warranting future sensory evaluation and validation across diverse water kefir grains.