As water and nutrient uptake should be related in the response of plants to salinity, the aim of this paper is to establish whether or not aquaporin functionality is related to H+‐ATPase activity in root cells of pepper (Capsicum annuum L.) plants. Thus, H+‐ATPase activity was measured in plasma membrane vesicles isolated from roots and aquaporin functionality was measured using a cell pressure probe in intact roots. Salinity was applied as 60 mM NaCl or 60 mM KCl, to determine which ion (Na+, K+ or Cl−) is producing the effects. We also investigated whether the effects of both salts were ameliorated by Ca2+. Similar results were obtained for cell hydraulic conductivity, Lpc, and H+‐ATPase activity, large reductions in the presence at NaCl or KCl and an ameliorative effect of Ca2+. However, fusicoccin (an activator of H+‐ATPase) did not alter osmotic water permeability of protoplasts isolated from roots. Addition of Hg2+ inhibited both ATPase and aquaporins, but ATPase also contains Hg‐binding sites. Therefore, the results indicate that H+‐ATPase and aquaporin activities may not be related in pepper plants.