Mungbean is one of the most powerful pulses providing substantial protein for human diets and fixing N to the soil, improving nutritional food security and agricultural sustainability. The production of summer mungbean in the tropics and subtropics is adversely affected by drought due to water scarcity caused by various factors as well as lack of rainfall. Irrigation at different growth phases is not a suitable solution. An environmentally friendly and economically viable answer is a convenient irrigation management option that will be available to farmers together with drought-tolerant genotypes. The study considered to determine the effect of differences between drought-tolerant and drought susceptible genotypes on water productivity response and physiological traits in mung beans. To quantify seed yield-related to irrigation at different growth stages eventually to quickly determine the most appropriate irrigation stage. One water stress tolerant mung bean genotype (BMX-08010-2) and one sensitive genotype (BARI Mung-1) were grown in the field with four different irrigation schedules along with water stress conditions (no irrigation) under rain shelter at Regional Agricultural Research Station, BARI, Ishwardi, Pabna, Bangladesh. The experiment was laid out in split plots with three replications, with irrigation schedules assigned in the main plot and mung bean genotypes assigned in the side plots. Water use efficiency ranged from 3.79 to 4.68 kg ha−1 mm−1 depending on irrigation regime, and mung bean seed yield of mung bean Water stress decreased plant water status, photosynthetic pigment and membrane stability index, and increased proline soluble sugar content. Treatments that received irrigation during two or three phases (I3 or I4) gave significantly higher yields than those that received irrigation during only one stage (I1 and I2) with the lowest yield. While the yield obtained ranged between 1145.44 kg ha−1 with seasonal irrigation of 277 mm (I4) and 555.14 kg ha−1 without irrigation (I0). The flowering stage (I3) was recorded as the most sensitive growth stage with an 18.15% yield reduction compared to the treatment with triple irrigation (I4). Also, depending on the irrigation sources, at least two irrigation phases should be provided at the triple leaf stage (I2, i.e., 20 DAS) and at the flowering stage (I3, i.e., 35 DAS) to achieve the highest yield. Genotypes that maintained the higher performance of physicochemical traits under water stress provided higher seed yield and promoted drought tolerance. Therefore, these parameters can be used as physiological and biochemical markers to identify and develop superior genotypes suitable for drought-prone environments.