Extensive research on salinity tolerance in rice has been mostly carried out at the seedling stage in single experimental trials. Here, we aimed to understand the roles of ion transport and oxidative responses of leaf mesophyll in salinity tolerance of rice (Oryza sativa L.) at its reproductive stage using comparative investigations in both greenhouse and field trials. Two experimental trials were conducted to assess the salt tolerance of three rice cultivars at their reproductive stage in greenhouse and field. We employed agronomic, physiological, electrophysiological, molecular and cell imaging techniques to compare physiological response of control and salinity stressed rice plants. Salinity had the most severe effect to Koshihikari, followed by Doongara and Reiziq. We found that K+ retention and low recovery Cl− efflux in mesophyll cells confers salt tolerance in rice. Moderate to strong correlations were found between growth parameters and net K+ flux (r2 = 0.45–0.60), and net Cl− flux (r2 = 0.47–0.72). Also, dynamic ROS production and regulation of the NADPH oxidase gene, OsRBOHD, in mesophyll cells is crucial for salt tolerance of rice at the reproductive stage. OsRBOHD expression was significantly correlated to recovery ion fluxes (r2 = 0.45–0.64). This study brings together, for the first time, potential links between cellular ionic stress and oxidative stress components of salinity tolerance in rice at the reproductive stage in both greenhouse and field conditions. Our study will provide guidance to examine crop salinity tolerance at reproductive stages in controlled environments and natural climatic conditions in the future.