A rotary disc filter is provided with an integrated backwash and chemical cleaning system. In one mode of operation, backwash is directed through a control valve to one or more nozzles for spraying the backwash onto the filter media forming a part of a rotary disc filter. In a second mode, a chemical cleaning mode, the pump directs backwash through an eductor that induces a chemical into the inductor which is mixed with the backwash to form a backwash-chemical mixture that is sprayed onto the filter media. A control system is used in conjunction with the backwash and cleaning systems to monitor process information and/or filter media properties and to determine when to perform backwashes and regenerative cleanings in order to optimize the performance of the filter system.