Membrane technology has been widely applied for water treatment, while membrane fouling still remains a big challenge. The polysaccharides in extracellular polymeric substances (EPS) have been known as a significant type of foulant due to their high fouling propensity. However, polysaccharides have many varieties which definitely behave differently in membrane filtration. Therefore, in this study, different polysaccharides alginate sodium and xanthan gum were chosen to study their effects on membrane fouling in a wide concentration range. The results demonstrated that the filtration behaviors of alginate sodium and xanthan gum were completely different, which was due to their different molecular structures. Alginate had a small molecular weight and it was easy for alginate to penetrate membrane pores resulting in pore blocking. A series of concentrations of alginate including 5 mg/L, 10 mg/L, 20 mg/L, 30 mg/L, 40 mg/L, and 50 mg/L were examined and it was found that the permeate flux decline highly depended on the level of alginate in the feed water. While for the filtration of xanthan gum, the same concentration of xanthan gum led to more serious fouling than that observed in alginate, which might be due to its large molecule. In addition, calcium chloride was added in the solutions of both alginate and xanthan gum to examine the influence of a divalent cation on polysaccharide fouling. A “unimodal” peak can be observed in the fouling propensity caused by Ca2+ and alginate with increasing the concentration of alginate. Such a phenomenon was not found in the fouling of xanthan gum and Ca2+ led to more serious fouling for all concentrations of xanthan gum. In light of this, this study gave new insights into the fouling propensities of different polysaccharides.