Physiological responses of tomato roots to NaCl and NaHCO₃ stresses were investigated in a hydroponic setting. The relative growth rate of tomato plants was significantly reduced in both NaCl and NaHCO₃ treatments, especially under NaHCO₃ stress. Tomato root respiration increased under low concentrations of NaCl and NaHCO₃ stresses. However, high concentrations of both NaCl and NaHCO₃ significantly inhibited respiration, especially in the NaHCO₃ treatment. With increasing concentration of NaCl and NaHCO₃ treatment, root Na accumulation increased, while accumulation of N, P, K, Fe, and Mg was significantly lower. Compared to NaCl, NaHCO₃ treatment resulted in more dramatic changes in these nutrients. All organic acids investigated were increased by NaHCO₃ after 5 days of treatment, but only oxalate, tartrate and malate were induced by NaCl. This implies that global regulation of organic acids might play an important role in tomato’s alkali stress tolerance. Compared to NaCl treatments, NaHCO₃ treatments induced much higher levels of reactive oxygen species (ROS) and lipid peroxidation after 5 days of treatment, which was accompanied by higher activities of antioxidant enzymes and higher concentrations of ascorbate–glutathione. However, after 10 days of treatment, 100 mM NaHCO₃ stress led to lower accumulation of ROS, antioxidant enzyme activities, and ascorbate–glutathione content. This may have been because root metabolism had almost completely stopped, as indicated by lower root respiration and activity.