Desalinated seawater (DSW) has emerged as a promising solution for irrigation in regions facing water scarcity. However, adopting DSW may impact the existing cultivation model, given the presence of potentially harmful elements, among other factors. A three-year experiment was carried out to assess the short-term effects of four irrigation waters—freshwater (FW), DSW, a mix 1:1 of FW and DSW (MW), and DSW with low boron (B) concentration (DSW–B)—on a ‘Rio Red’ grapefruit orchard. These irrigation waters exhibited varying levels of phytotoxic elements, some potentially harmful to citrus trees. Sodium (Na+) and chloride (Cl−) concentrations exceeded citrus thresholds in all treatments, except in DSW−B, whilst B exceeded toxicity levels in DSW and MW treatments. Leaf concentrations of Cl− and Na+ remained low in all treatments, whereas B approached toxic levels only in DSW and MW–irrigated trees. The rapid growth of the trees, preventing excessive accumulation through a dilution effect, protected the plants from significant impacts on nutrition and physiology, such as gas exchange and chlorophyll levels, due to phytotoxic elements accumulation. Minor reductions in photosynthesis in DSW–irrigated trees were attributed to high B in leaves, since Cl− and Na+ remained below toxic levels. The accelerated tree growth effectively prevented the substantial accumulation of phytotoxic elements, thereby limiting adverse effects on tree development and yield. When the maturation of trees reaches maximal growth, the potential accumulation of phytotoxic elements is expected to increase, potentially influencing tree behavior differently. Further study until the trees reach maturity is imperative for comprehensive understanding of the long-term effects of desalinated seawater irrigation.