This study investigated the effectiveness of infrared thermography to estimate water status in Merlot and Moscato grown in northeast Italy by comparing the crop water stress index (CWSI) and the stomatal conductance index (IG). The influence of the portion of the canopy in which the thermal images were captured (sunlit or shaded) was also investigated. During the 2018 growing season, potted vines were subjected to three irrigation treatments: T0 = 100% of daily water usage restored; T1 = 50% of daily water usage restored; and T2 = 30% of daily water usage restored. Measurements included stomatal conductance (g_s), stem water potential (SWP), and thermal imagery. Results showed that both the CWSI and IG indices were effective in discriminating the irrigation treatments in Moscato and Merlot. CWSI showed higher correlations with g_s and SWP compared to IG, especially in Moscato. CWSI was less influenced by the portion of the canopy the image was taken on. In general, Moscato showed greater differences in g_s, SWP, and the thermal indices between the three irrigation treatments. This study suggests that the efficacy of thermography in estimating vine water status depends on the variety and its stomatal control physiology.