Wheat (Triticum aestivum L.) breeding programs strive to increase grain yield (GY), yet, progress is hampered due to quantitative inheritance, low heritability, and confounding environmental effects. This study identified QTL associated with GY with the goal of improving GY by pyramiding GY-QTL with QTL associated with CID, plant height (HT), days to heading (HD).  To identify GY QTL, we evaluated a winter wheat population of 159 recombinant inbred lines (RIL) in three field conditions, rain-fed (RF), terminal drought (TD, water stress applied after anthesis), and fully irrigated (IR), with a total of six location-year environments. Four QTL associated with GY were identified under the three field conditions and mapped on chromosome arms 1BS, 3BS, 3BL and 4BL. The four QTLs have additive effects towards increasing GY and accumulation of the favorite alleles of the four QTL could increase grain yield up to 17%. Carbon isotope discrimination (CID) has been proposed as good criteria for grain yield improvement under drought. CID was evaluated in two years (2009 and 2010) with three different plant tissues flag leaf (2009 and 2010), glumes (2009), and grain flour (2010). A total of seven QTLs were detected on seven chromosomes (1A, 1B, 2B, 3A, 6B, 6D and 7A) with R² arranging from 7% to 13%. The 1BS QTL associated with GY not only affects CID under RF, but also HD under RF and TD. The 3BL QTL associated with HT under IR, and the 4BL QTL that located at the region containing Rht-B1 locus also contributed to HT under all three conditions.  The 2BS QTL associated with CID affects HD under all three conditions. This study suggests that plant height and photo-responsive genes plays an important role in plant adaptation, yield performance, and drought tolerance.