A heat source system includes heat source apparatuses each with refrigerant circuit and water heat exchanger. A water supply header pipe merges and supplies, to a load, water flowing in from the heat exchangers. A water return header pipe splits, into the heat exchangers, water flowing in from the load. Pumps feed water to the heat exchangers. A bypass pipe with bypass valve connects the supply and return header pipes. A differential pressure gauge measures a water pressure difference between supply and return. A controller determines the number of heat source apparatuses to operate, from heat generated by refrigerant circuits and heat required, determines whether an operating frequency of the pump connected to a heat source apparatus to be operated is a minimum frequency, and controls the pump operating frequency and/or an opening degree of the bypass valve such that the water pressure difference falls within a target range.