Intra-seasonal drought episodes during the life cycle of plant growth of sesame affect physiological quality of seeds harvested. For this purpose, in this study, we explored the following water treatments: W1 (Irrigation throughout the cycle, non-stress treatment), W2 (water stress at the vegetative growth phase), W3 (water stress at the flowering to early pod formation), W4 (water stress at the fruit maturation phase) and W5 (water stress in all phases); for their effect on germination capacity and seedling from the produced seeds of four sesame varieties (“SN 203”, “SN 403”, “SN 01-06” and “Ngong”). Such studies allowed evaluating the performance of the seeds harvested from the plants subjected to water stress availability during the different phenological phases of each variety. The produced seeds were evaluated by reduction rate (%) of germination percentage, first germination count, germination speed index, mean germination time, coefficient of velocity of germination, seedling emergence, seedling length, seedling fresh weight and seedling dry weight. In general, sesame seeds from plants grown under water deficit display reduction in performance. In water stress at the fruit maturation phase (W4) and water stress in all phases (W5), the sesame varieties tested are more sensitive for both germination capacity and seedling and for seedling respectively; so that water limitation during these periods results in the production of seeds with reduction in performance more intense. Among the varieties tested, “SN 01-06” and “Ngong” were the most tolerant genotypes. These results will be used for extension of sesame and for genetic improvement program.