In light of the increasing demand for resilient crops amid global food security concerns, recent advances in omics technologies have accelerated plant breeding efforts. Nonetheless, their effectiveness is often undermined by limited phenotypic resolution, particularly under field conditions. Traditional approaches based on single daily measurements are insufficient to capture the full spectrum of genotypic responses, especially when environmental stress is present. This study explores the potential of thermal imaging using unmanned aerial vehicles (UAVs) to monitor canopy temperature (CT) in wheat, providing a non-invasive proxy for assessing plant water status. A collection of 184 genetically distinct wheat genotypes was examined under both irrigated and rainfed conditions within a Mediterranean agroecosystem. Thermal data were recorded across multiple phenological phases (from anthesis to grain filling) and at various times throughout the day. The analysis revealed that both developmental stage and time of observation substantially influenced CT patterns, thereby impacting the detection of genotype-specific responses to drought. The most pronounced thermal contrasts between irrigation regimes were observed during the milk-dough and dough stages, particularly in the mid-afternoon when vapor pressure deficit (VPD) reached its peak. These insights support the integration of diurnal thermal phenotyping into breeding pipelines as a means to enhance the identification of drought-adaptive traits in cereal crops.