Drought and salinity stresses will have a high impact on future crop productivity, due to climate change and the increased competition for land, water and energy. The response to drought (WS), salinity (SS) and the combined stresses (WS+SS) was monitored in two maize lines: the inbred B73 and an F1 commercial stress-tolerant hybrid. A protocol mimicking field progressive stress conditions was developed and its effect on plant growth analyzed at different time points. The results indicated that the stresses limited growth in the hybrid and arrested it in the inbred line. In SS, the two genotypes had different ion accumulation and translocation capacity, particularly for Na+ and Cl-. Moreover, the hybrid perceived the stress, reduced all the analyzed physiological parameters, and kept them reduced until the recovery. B73 decreased all physiological parameters more gradually, being affected mainly by SS. Both lines recovered better from WS than the other stresses. Molecular analysis revealed a diverse modulation of some stress markers in the two genotypes, reflecting their different capacity to cope with stresses. Combining biochemical and physiological data with expression analyses yielded insight into the mechanisms regulating the different stress tolerance of the two lines.