Sea buckthorn (Hippophae rhamnoides L.) is consumed mainly in its processed form. Therefore, the investigation of the physicochemical properties of its berries is a current task in the aspect of food processing. The aim of this study was to determine the physicochemical parameters (soluble solid content, total titratable acidity, sugar/acid ratio), color characteristics (L*, a*, b*) and fatty acid profile of five varieties (‘Askola’, ‘Clara’, ‘Habego’, ‘Leikora’, ‘Mara’) and one Hungarian candidate, R-01, to establish a basis for experiments on the processability of the whole berries (e.g., drying). The weight of the berry of ‘Leikora’ (0.64 g) was significantly higher than the other investigated fruits. The differences between the values of soluble solid content (6.3–10.84 °Brix) and titratable acid (1.4–3.7%) content of berries were significant. ‘Mara’ had the highest sugar/acid ratio. Regarding the fatty acid profile, the amount of unsaturated fatty acids was measured between 72.6–83.4%, including polyunsaturated fatty acids, which were between 32.3–58.1%. The seeds of the tested samples contained high concentrations of linoleic acid (17.0–33.2%) and linolenic acid (15.3–24.9%), mainly in the case of the ‘Mara’, ‘Clara’ and ‘Askola’ varieties. Candidate R-01 could be used as a raw material for functional foods due to its significant content of palmitoleic acid and a favourable omega-6/omega-3 ratio.