SummarySignificant acute cardiovascular, metabolic, and endocrine changes have been traced to short-lasting cold water immersion (CWI); however, the long-term impact of recurrent CWI on atherogenesis, lipid parameters, and fat distribution has not yet been studied. The goal of this study was to investigate the alleged protective effect. A total of 35 healthy volunteers were monitored for a period of 5 months during which the CWI was performed under standardized conditions (three times per week for 7–10 min, without neoprene equipment). Volunteers with measured weight or muscle mass increases of more than 5% were ineligible. An analogous control group (N = 30) was included. At the onset and completion of the study, blood samples were obtained, and clinical assessments took place. PCSK9 and hsCRP levels were measured together with other lipid-related and non-lipid-related indicators. Carotid intima-media thickness test (cIMT) and echo-tracking for the identification of arterial stiffness (PWV, AI, and β) were used to identify early vascular alterations. Hepatorenal index (HRI) calculations served to quantify liver steatosis, while changes in subcutaneous and visceral fat thickness were used to quantify fat distribution. The given protocol was successfully completed by 28 volunteers. Long-term repeated CWI resulted in a significant decline in cIMT (p = 0.0001), AI (p = 0.0002), Beta (p = 0.0001), and PWV (p = 0.0001). PCSK9 (p = 0.01) and hsCRP (p = 0.01) showed a significant decrease when compared to initial values. In comparison to the starting values, liver fat accumulation decreased by 11% on average (HRI p = 0.001). LDL, TC, TG, and VLDL levels all significantly decreased as well. We suggest that repeated CWI may have beneficial impact on lipid, non-lipid, and lipid-related indices, as well as atherogenesis and liver fat storage.