This study tests the diurnal variations of water status, leaf gas exchanges and chlorophyll fluorescence in Pistacia vera L. (P. vera L.) and Pistacia atlantica Desf. (P. atlantica Desf.) seedlings. At 40% of field capacity, diurnal variations in water uptake, relative water content (RWC) were estimated every hour between 5:00 am and 7:00 pm. The daily course of light, temperature, photosynthesis (A), stomatal conductance (gs), transpiration rate (E), intrinsic water use efficiency (A/gs), mesophyll efficiency (A/Ci), internal CO2 concentration (Ci) and chlorophyll fluorescence were measured every 3 h from 05:30 am to 7:30 pm in irrigated and stressed seedlings of the two studied species. The results showed a significant variation in all surveyed parameters over diurnal cycle. The stressed seedlings of P. atlantica exhibited considerably higher RWC, water uptake, A, gs, E, A/gs and A/Ci over diurnal cycles compared to P. vera stressed seedlings. In contrast, P. vera was more sensitive to water stress and excess light and temperature over the diurnal cycle. The midday stomatal conductance and photosynthesis decrease was more likely the result of low RWC caused by high transpiration rates, stomatal closture and photoinhibition. Photoinhibition is a protective mechanism of PSII, rather than a result of photo-damage of photosynthetic apparatus. P. atlantica revealed an important physiological feature that is maintaining photosynthesis at midday compared to P. vera. This might be due to internal regulation through several mechanisms mainly better osmotic adjustment, photoprotective mechanisms of PSII.