Salt stress is a major limiting factor in avocado (Persea americana) cultivation, exacerbated by global trends towards scarcity of high-quality water for irrigation. Israeli avocado orchards have been irrigated with relatively high-salinity recycled municipal wastewater for over three decades, over which time rootstocks were selected for salt-tolerance. This study’s objective was to evaluate the physiological salt response of avocado as a function of the rootstock. We irrigated fruit-bearing ‘Hass’ trees grafted on 20 different local and introduced rootstocks with water high in salts (electrical conductivity of 1.4–1.5 dS/m). The selected rootstocks represent a wide range of genetic backgrounds, propagation methods, and horticultural characteristics. We investigated tree physiology and development during two years of salt exposure by measuring Cl and Na leaf concentrations, leaf osmolality, visible damages, trunk circumference, LAI, CO2 assimilation, stomatal conductance, spectral reflectance, stem water potential, trichomes density, and yield. We found a significant effect of the rootstocks on stress indicators, vegetative and reproductive development, leaf morphogenesis and photosynthesis rates. The most salt-sensitive rootstocks were VC 840, Dusa, and VC 802, while the least sensitive were VC 159, VC 140, and VC 152. We conclude that the rootstock strongly influences avocado tree response to salinity exposure in terms of physiology, anatomy, and development.