With increasing surface water shortage for irrigation, brackish water is increasingly used for irrigating a variety of crops in arid and semi-arid agroecosystems. This study evaluated the impacts of brackish water irrigation on gas exchange and water uptake in tomato plants and proposed a new model to predict responses of tomato evapotranspiration and yield to irrigation water salinity. A greenhouse experiment was conducted under five salinity treatments: tap water of EC 0.6, brackish water of EC 2 and 3, and reserve osmosis (RO) concentrate of EC 4 and 6 dS m−1. Results indicated that increasing water salinity reduced plant evapotranspiration (ET) and consequently increased deep percolation (DP) and leaching fraction (LF). Tomato yield decreased with increasing salinity, but moderate salinity (2 dS m−1) stimulated leaf photosynthesis rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs). The increasing salinity of irrigation water increased Na and Mg but decreased K and Ca accumulations in plants. The accumulations of micronutrients (Fe, Mn, Cu, B, and Al) except Zn in the whole plant decreased with increasing salinity. Tomato yield was significantly correlated to accumulations of Na, Ca, P and N in whole plants. The proposed new model provided a good estimation of both yield and ET under saline conditions. The calculated soil salinity threshold values of ECe* from the new model were 1.73 dS/m for yield and 2.52 dS/m for ET, respectively, indicating that the reduction of tomato yield was more sensitive to salinity than the decrease of ET. To achieve an optimal comprehensive plant growth and nutrition, this study showed that tomato plants can be irrigated up to a water salinity of 2 dS m−1 without causing stress.