Salinity is a serious issue for crops, as it causes remarkable yield losses. The accumulation of Na+ affects plant physiology and produces nutrient imbalances. Plants trigger signaling cascades in response to stresses in which phytohormones and Ca2+ are key components. Cation/H+ exchangers (CAXs) transporters are involved in Ca2+ fluxes in cells. Thus, enhanced CAX activity could improve tolerance to salinity stress. Using the TILLING (targeting induced local lesions in genomes) technique, three Brassica rapa mutants were generated through a single amino acidic modification in the CAX1a transporter. We hypothesized that BraA.cax1a mutations could modify the hormonal balance, leading to improved salinity tolerance. To test this hypothesis, the mutants and the parental line R-o-18 were grown under saline conditions (150 mM NaCl), and leaf and root biomass, ion concentrations, and phytohormone profile were analyzed. Under saline conditions, BraA.cax1a-4 mutant plants increased growth compared to the parental line, which was associated with reduced Na+ accumulation. Further, it increased K+ concentration and changed the hormonal balance. Specifically, our results show that higher indole-3-acetic acid (IAA) and gibberellin (GA) concentrations in mutant plants could promote growth under saline conditions, while abscisic acid (ABA), ethylene, and jasmonic acid (JA) led to better signaling stress responses and water use efficiency. Therefore, CAX1 mutations directly influence the hormonal balance of the plant controlling growth and ion homeostasis under salinity. Thus, Ca2+ signaling manipulation can be used as a strategy to improve salinity tolerance in breeding programs.