The aim of the study was to evaluate wheat flour fractions and the relationships between the rheological properties of wheat flour mill streams with arabinoxylans content to predict flour functionality. The tested wheat variety was IS Laudis and an industrial milling station with several roll sections was employed to reach 30 passages of flour streams. Each mill stream fraction was analyzed separately. Several physiochemical (moisture, ash content, falling number, wet gluten content, gluten index, and damaged starch content) and rheological properties were evaluated by means of utilizing various test apparatus and techniques. The total content of non-starch polysaccharides and arabinoxylans, as well as soluble and insoluble fractions were investigated. Results showed significant differences between the mill streams in terms of the content of physicochemical parameters and rheological properties, as well as in soluble and insoluble fractions of non-starch polysaccharides and arabinoxylans. The relationships between the tested parameters and PCA analysis can be useful for millers who can then select and blend several flour streams to obtain a maximum amount of flour with specified characteristics. A better understanding of the origin and function of different fractions and the role of arabinoxylans and their fractions in the milling process will allow the development of wheat flour blends with the desired functionality. Flours from late reduction and sizing passages (C and R) as well as from sorting filter (V) streams showed high ash content as well as T-NSP and T-AX levels, so the final content of NSP in flour blends may be balanced by the application of the proper amount of C6–C7 and R5 stream flours.