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Despite the well-known cutaneous beneficial effect of thermal water on the skin, no data exist regarding the potential biological effect of orally consumed water on healthy skin. Thus, in this single-center, double-blind, randomized controlled clinical trial conducted on age and menstrual cycle timing-matched healthy female volunteers (24 + 24) consuming water A (oligo-mineral) or water B (medium-mineral) for 1 month (T1), the cutaneous lipidomics were compared. Interestingly, only water A consumers had a statistically significant (p < 0.001) change in cutaneous lipidomics, with 66 lipids different (8 decreased and 58 increased). The cutaneous lipidomics of consumers of water A vs. water B were statistically different (p < 0.05). Twenty cutaneous lipids were necessary to predict the water type previously consumed (AUC ~70). Our study suggests that drinking oligo-mineral water may change skin biology and may influence the cutaneous barrier, so future dermatological clinical trials should also account for the water type consumed to avoid potential confounders.