Mungbean is susceptible to waterlogging stress; therefore, breeding tolerant varieties would provide Australian growers with management options for wet summer season planting. Selection for waterlogging tolerance could be improved using vegetative indices that correlate to yield. Five mungbean genotypes were exposed to waterlogging stress at the pod-filling stage and characterised for various morphological and physiological traits governing seed yield. Waterlogging during pod filling decreased stomatal conductance (gs) and photosynthetic rate (Asat) to ~27% and 25% compared to control, respectively, resulting in a decline in effective quantum yield of PSII (ФPSII) and maximum efficiency of PSII of dark-adapted leaves (Fv/Fm) and leaf chlorophyll while increasing excitation pressure (1-qP) significantly. Waterlogging at pod filling reduced leaf count (19%), plant height (23%), leaf dry weight (38%), stem dry weight (33%), pod dry weight (36%), above-ground biomass (34%), root biomass (26%), and 100-seed weight (4%). Seed yield was highly positively correlated with Asat (0.86), gs (0.69), chlorophyll content (0.63), and ФPSII (0.59), with a highly negative correlation with 1-qP (−0.87) at 30 days of treatment imposition. A yield penalty of 32% was recorded under waterlogging stress compared to control plants, while the performance of all genotypes was found to be similar in terms of seed yield. Interestingly, genotype AVTMB#3 produced significantly larger seeds under waterlogging stress relative to other genotypes, including the leading Australian mungbean variety, Jade-AU. Based on a robust and significantly strong correlation with seed yield under waterlogging stress, 1-qP and photosynthetic rates (Asat) are recommended as potential indicators for the screening of mungbean genotypes. Thus, the current study presents a framework for screening waterlogging tolerance, which can provide a reasonable basis for the selection of various genotypes in future mungbean breeding programs.