The forms of water transportation, arrangement and operation of pumps contribute to the water transportation energy consumption, which influences the energy-saving effect of surface water source heat pump. The relation between the pumping height and energy consumption of pumps is found by analyzing the model of pump energy consumption. The concept and calculation of critical pumping height is presented considering the limited rate of system energy efficiency. Based on the principle that the pump power changes with water flow rate, the determination of pumps arrangement of one or two stage pumps is described with a concrete example. The influence of water flow rate on heat pumps and water pumps is analyzed, and the energy efficiency of constant and variable water volume are compared. The operation way of this example is concluded for the optimal system energy efficiency. It is found that there is a critical pumping height for the energy-saving effect of surface water source heat pump compared with the traditional system. Moreover, the operation strategies should be determined by the system optimal model since the energy consumptions proportions of heat pumps and water pumps are variable.