Chitosan membranes were prepared by the casting method combined with alkali treatment. The molecular weight of chitosan and the alkali treatment influenced the water content and water permeability of the chitosan membranes. The water content increased as the NaOH concentration was increased from 1 to 5 mol/L. The water permeation flux of chitosan membranes with three different molecular weights increased linearly with the operating pressure and was highest for the membrane formed from chitosan with the lowest molecular weight. Membranes with a lower water content had a higher water flux. The membranes blocked 100% of compounds with molecular weights above methyl orange (MW = 327 Da). At 60 ≤ MW ≤ 600, the blocking rate strongly depended on the substance. The results confirmed that the membranes are suitable for compound separation, such as in purification and wastewater treatment.