Solar Photovoltaic Water Pumping (SPVWP) systems have established their potential as the most dependable and economically viable systems compared to the diesel based or grid-based electrical pumps. This paper presents an in-depth investigation of the energy efficiency of SPVWP system based on solar radiation, temperature, and operational heads. The study also identifies the shortcomings in the conventional design method based on Best Efficiency Point (BEP) concept that is applicable only in case of fixed frequency and voltage type pumps. However, in the case of SPVWP systems, due to variations in the solar intensity, ambient temperature, and water head, BEP concept does not offer the best efficiency design. The study experimentally proves that the model based on weighted system efficiency and Solar Operational Duty Head (SODH) increases the performance of SPVWP system (∼9% gain) and is consistently provide higher efficiencies in any season or under any climatic conditions. •Energy efficiency of SPVWP system is investigated to find the shortcomming in the conventional design method of SPVWP system.•Best efficiency concept for selection of motor-Pump, misleads on overall energy efficiency, leads to losses.•BEP method of selection of motor-pump set is applicable only in case of fixed frequency and voltage type grid supply.•Study guides the selection of a proper pump based on the new concept Solar Operational Duty Head (SODH).•About 9 % gain in water output is observed through the new concept Solar operational Duty Head.