Rice yield reduction due to water limitation depends on its severity and duration and on the phenological stage of its occurrence. We exposed three contrasting rice genotypes, IR64, UPLRi7 and Apo (adapted to lowland, upland and aerobic conditions, respectively), to three water regimes (puddle, 100% and 60% field capacity) in pots during the vegetative (GSI), flowering (GSII) and grain filling (GSIII) stages. Stress at all the three stages significantly reduced yield especially in lowland genotype IR64. Effect of water limitation was more severe at GSII than at the other two stages. Stress at GSI stage reduced both source activity (leaf area and photosynthetic rate) and sink capacity (tiller number or panicle number per pot). When stress was imposed at GSII, spikelet fertility was most affected in all the three genotypes. In both GSII and GSIII, although leaf area was constant in all the three water regimes, estimated relative whole-plant photosynthesis was strongly associated with yield reduction. Reduced photosynthesis due to stress at any given stage was found to have direct impact on yield. Compared to the other genotypes, Apo had deeper roots and maintained a better water relation, thus, higher carbon gain and spikelet viability, and ultimately, higher biomass and productivity under water-limited conditions. Therefore, screening for these stage-dependent adaptive mechanisms is crucial in breeding for sustained rice production under water limitation.