<p>In coastal ecologies, salinity and flooding impede rice plant growth and development. To identify the differential effects of the combined salinity and stagnant flooding stress from their individual effects, an experiment was conducted with twelve rice genotypes by subjecting them to salinity, flooding, and saline water flooding stresses. Based on the impact on grain yield, stress tolerance indices, and other key physiological traits, we found that the combined saline water and flooding were more detrimental to rice plants than their individual effects. Genotypes like Gangasiuli, Rashpanjor, AC39416A, and FR13A that were tolerant to both salinity and flooding stresses also performed better under combined stresses of saline water flooding. However, genotypes like FL478, SR26B, and AC39293, which were tolerant to salinity but susceptible to flooding stress, were found to be highly susceptible to combined stresses of saline water flooding. Interestingly, the genotype Ravana, which was tolerant to flooding but susceptible to salinity stress, was found to be moderately tolerant to combined stress. The dynamics of K⁺ and Na⁺ in different plant parts (particularly in the leaf, leaf sheath, and stem) suggested that a dominant role of K⁺-retention, rather than management of upward Na⁺ transport, is more important for withstanding the individual and combined stresses of saline water flooding in rice. Additionally, high selective transport of K⁺ over Na⁺ from root to upper plant parts played a key role in tolerating both salinity and combined stresses. Overall, we identified that tolerance to flooding stress, rather than salinity, was more important in tolerating the combined stresses of saline water flooding in rice.</p> Graphical abstract <p></p>