Hydrophobically-modified chitosan (HC) has emerged as a promising flocculant for trace pharmaceutical removal from surface water. However, the variation in the characteristics of dissolved organic matter (DOM) in different water sources influences the efficacy of HC in removing pharmaceutical compounds. In this work, the flocculation performance of sequentially dosing alum and HC (alum+HC) for the treatment of five water types (three synthetic waters, and samples of two real waters collected from the Yangtze River and the Thames River), having different DOM and five representative pharmaceuticals (initial concentration: 100 ng/L), was assessed by bench-scale jar tests. The DOM characteristics were correlated quantitatively with the removal efficiencies (REs) of the pharmaceuticals. Density functional theory computations were performed to illuminate the interfacial interactions in the flocculation. Alum+HC exhibited a remarkably higher RE of all five pharmaceuticals (maximum RE: 73%-95%) from all waters compared to a conventional coagulant or flocculant (alum or polyacrylamide, respectively). In contrast to using HC alone, alum+HC also achieved a higher RE of pharmaceuticals with nearly half the HC dosage, thereby enhancing the cost-effectiveness of the alum+HC dosing system. Among the different key DOM characteristics, the surface charge and molecular weight of DOM had no evident correlation with RE(pharmaceutical), but the hydrophobic/hydrophilic nature and functional group composition of organic carbon of DOM were strongly correlated: Strongly hydrophobic fractions, with C-C & C=C functional groups (binding pharmaceuticals via hydrophobic association), were beneficial, while hydrophilic fractions with C-OH groups were less effective, for pharmaceutical removal. This work showed the enhanced performance of the alum+HC dosing combination in the removal of different pharmaceutical compounds from different waters, and filled the knowledge gap regarding the performance of hydrophobically-modified flocculants in the treatment of different surface water sources.