Net photosynthesis rate and drought resistance in wheat need to be improved to enhance overall wheat productivity. Association mapping was used to explore the potential QTLs associated with net photosynthesis rate (Pn), thousand-kernel weight (TKW), biomass plant -1 (BMPP) and grain yield plant -1 (GYPP) under two water conditions and their drought indices, i.e. stress tolerance index (STI) and stress susceptibility index (SSI) in wheat using 269 whole-genome SSR markers in 59 winter wheat genotypes. Large numbers of marker-trait associations (MTAs) were detected for photosynthesis and yield related traits under both water conditions and related drought tolerance indices in both seasons. However, the number of significant associations reduced greatly when Bonferroni correction (FPDR) test was applied. Single marker, i.e. Xpsp3123-7D was associated with multiple traits across moisture conditions as well as growth seasons. Xgwm182-5D was stably associated with TKW under water-stressed conditions and with GYPP under well-watered conditions, respectively in both seasons. Xcfd33-6D was consistently linked with BMPP in both seasons under well-watered condition. A Total of 28 associations for the drought tolerance indices of those phenotypic traits qualified FPDR test. Of these, Xpsp3123-7D was consistently associated with the two drought indices of the traits in two seasons. The markers Xwmc707-4A and Xgwm182-5D were stably associated with stress susceptibility index (STI) of BMPP and stress tolerance index (STI) of TKW, respectively across two seasons. These putative QTLs, especially Xpsp312-7D can be the key targets to improve photosynthetic efficiency and yield potential of bread wheat in rainfed ecosystem.