Many low-lying coastal areas worldwide, including Florida, experience soil salinization due to tropical rainstorms, storm surges that cause superficial flooding with saline water, and groundwater salinization from saltwater intrusion. Additionally, excessive fertilizer applications can increase soil salinization, which can reduce the productivity of soil and affect crop growth. This study evaluated the response to salinity stress of two peach rootstocks: 1) Flordaguard, the current recommended rootstock in Florida, and 2) MP-29, a peach-plum hybrid rootstock with the potential to be recommended in the state. A total of 60 plants were distributed in five blocks and exposed to three salinity levels (0, 75, and 150 µM NaCl) for 24 days in a greenhouse. Photosynthetic rate (A), stomatal conductance (gs), and efficiency of photosystem II (ΦPSII) were recorded every other day. Stem water potential (Ψs) and foliar nutrient concentrations were assessed at the end of the experiment. A decline in A level was observed in all plants over time, with a higher reduction under salinity treatments. Starting 16 days after treatment, gs was significantly lower in plantlets exposed to 150 µM NaCl compared to controls. Interestingly, ΦPSII was more stable in Flordaguard plants during the experiment. Moreover, ΦPSII response suggested higher sensitivity to salinity in MP-29 plants. Similarly, Ψs in salinity stressed plants was at least 33% lower compared to the control group. On the other hand, Ψs in ‘MP-29’ was 11% lower compared to ‘Flordaguard’, indicating higher water stress in the hybrid rootstock. Foliar nutrient concentrations were influenced by treatment (N), cultivar (Ca, B, Mn, Zn), or their interaction (Mg, S), while P, K, Fe, and Cu remained unchanged. These results suggest that MP-29 rootstock is more sensitive to salinity stress than Flordaguard, which may have implications for rootstock selection in saline-prone soils.