Synthetic polyelectrolyte are used in water and wastewater treatment systems as coagulant and filtration aids. Most of these polymers do not have a short term biodegrable property and some of them cause cancer and genetic mutation in human. In this study, the performance of different natural polyelectrolytes, as replacement materials for synthetic polyelectrolytes, in water treatment and effective parameters on their performance were evaluated. As a result, a suitable operational condition for water treatment was determined. The experimental results showed that biopolymers such as chitosan, sodium alginate and starch can be used as coagulating aid in water treatment system for reduction of turbidity. In comparison with starch and sodium alginate, chitosan has better performance for reduction of turbidity and besides, its operational range is wider. Also, the coagulated particles were bigger and stronger than those resulting from starch and sodium alginate. Therefore, using chitosan is more effective in settling and clarification operations of water treatment.