The effects of some nongenetic factors on milk protein fraction contents and relative proportions were estimated in 606 individual milk samples of Mediterranean water buffalo. Content of αS1-casein (CN), αS2-CN, β-CN, γ-CN, κκ-CN, glycosylated κ-CN (glyco-κ-CN), α-lactalbumin, and β-lactoglobulin was measured by reversed-phase HPLC. Relative contents of αS1-CN%, αS2-CN%, β-CN%, and κ-CN% were, respectively, 32.1, 17.1, 34.5, and 15.7%, whereas γ-CN% accounted for 0.6% of total casein content. Increasing total casein content in milk would result in a greater proportion of β-CN% at the expense of all of the other major casein fractions, especially of κ-CN%. Values of αS2-CN%, β-CN%, and γ-CN% tended to decrease with parity, although their variations were not significant, whereas αS1-CN% and glyco-κ-CN% showed the opposite trend. Contents of most protein fractions showed the typical trends observed for milk components as lactation progressed, with high contents in early lactation, a minimum in midlactation, followed by a gradual increase toward the latter part of lactation. Values of αS1-CN% increased during lactation, whereas αS2-CN% decreased. The proportion of β-CN% had its maximum value between 60 and 160d of lactation, followed by a decrease, whereas κ-CN% had its minimum value in early lactation (<60d) and remained relatively constant in the period of mid and late lactation. Glyco-κ-CN% and β-lactoglobulin% decreased in the first part of lactation, to reach their minimum values in midlactation, followed by an increase. Milk of top-producing buffaloes, compared with that of low-producing ones, had a significantly greater value of β-CN% and glyco-κ-CN%, and lower proportion of αS1-CN%. The possible effect exerted by protein genetic variants in affecting variation of milk protein fraction contents and relative proportions should be further considered to better get insight into buffalo milk protein composition.