Stagnant flooding (SF) is a serious threat for rice production in rainfed lowland areas of Southeast Asian countries. To overview the SF effect, photosynthetic performances and productivity were studied with three landraces (Ravana, Kamini, and Rashpanjor) and four high-yielding cultivars (Savitri, Savitri-Sub1, Gayatri, and Varshadhan) of rice under medium depth (40-50 cm) of water level. Stagnant flooding significantly increased the stem elongation and decreased yield and yield attributing parameters. The chlorophyll a fluorescence rises from O-to P-step with distinct J-and I-step were noticed in all the cultivars up to 75 d of SF. Prolonged flooding (> 2 months) perturbed both donor and acceptor side of PSII. Vitality indices (PIABS and PITOT) decreased greatly under prolonged SF. Analysis of O-J-I-P transients suggests that the information is useful for agricultural planning with the purpose to enhance rice yield under lowland medium depth SF.