Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs),Sub1, for submergence andPup1for low phosphorus stress tolerance along with narrow-grained trait,GW5were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1generation, respectively. Recurrent parent’s genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in theSub1andGW5QTLs carrier while a segmentwas observed in thePup1carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.