Canopy temperature (CT), chlorophyll content index (CCI), and flag leaf senescence (FLS) are important physiological traits related to drought tolerance of wheat. In order to dissect their genetic basis, a mapping population of 159 recombinant inbred lines (RILs) from ‘Rio Blanco’ by ‘IDO444’ was evaluated in four different water stressed environments over 3 years. Using an established genome wide genetic map, composite interval mapping was conducted to estimate QTL and their effects. A total of 16 QTL were detected on 8 of the 21 chromosomes, including 2 QTL for CT on chromosome 2A and 3A, 3 QTL for FLS on chromosome 2B, 5B and 7B, and 11 QTL for CCI on chromosome 2D, 3A, 3B and 4B. These QTL explained 7.3% to 25.9% of phenotypic variation. Seven and three QTL were located on chromosomes 2D and 3A, respectively. The QTL cluster on chromosome 2D is associated with CCI under three environments; while the QTL cluster on 3A associated with CCI in two environments and CT in one environment. Correlation analysis suggests that phenotyping of physiological traits were affected by heading date and plant height and their effects varied under different environments. This study identified QTL of some important physiological traits and the consistency of some QTL x reveals their potential for marker-assisted selection in diverse environments.