There are few studies that evaluate the application of chitosan in the treatment of eutrophic waters and its contribution to disinfection by-product formation. Thus, this study evaluated the use of chitosan as coagulant in the treatment of lake water spiked, or not, with Microcystis aeruginosa cells, as well as the formation of trihalomethanes (THM) by chlorine oxidation. Coagulant doses were from 0 to 9 mg/L of chitosan, and from 0 to 18 mg/L of aluminum sulfate (Al2(SO4)3), used as a comparative base. The THM formation was measured in filtered water after 48 hours of oxidation. The results showed that chitosan can provide effective removal of turbidity, apparent color, absorbance at 254 nm and chlorophyll a (M. aeruginosa cells), presenting better results than aluminum sulfate. No THM were detected after oxidation with chlorine, regardless of the coagulant used, suggesting that the use of chitosan as coagulant, for the studied waters, did not contribute to THM formation.