This study examined the percentage and stable isotope ratios of fatty acids in milk to study seasonal, year, and regional variability. A total of 231 raw cow milk samples were analyzed. Samples were taken twice per year in 2012, 2013, and 2014, in winter and summer, covering four distinct geographical regions in Slovenia: Mediterranean, Alpine, Dinaric, and Pannonian. A discriminant analysis model based on fatty acid composition was effective in discriminating milk according to the year/season of production (86.9%), while geographical origin discrimination was less successful (64.1%). The stable isotope composition of fatty acids also proved to be a better biomarker of metabolic transformation processes in ruminants than discriminating against the origin of milk. Further, it was observed that milk from Alpine and Mediterranean regions was healthier due to its higher percentage of ω-3 polyunsaturated fatty acid and conjugated linoleic acid.