Rice genotype (cv. Swarna Sub1) was compared with cv. Swarna with respect to salinity stress. The modality of sub1A traits, which is primarily linked to submergence tolerance, was monitored as to its sensitivity to salinity. Proline and electrolyte leakage were not significantly changed in cv. Swarna Sub1 as compared to cv. Swarna. However, the effects of silver ions through individual, hydroponics and pre-treatment distinctly varied between two cultivars. Silver absorption distinctly varied with 45.01-fold rises in cv. Swarna against control, whereas for sodium cv. Swarna Sub1 scored the highest accumulation by 3.03-fold. Potassium depletion in plants recorded a significant down-regulation for both the genotypes, maximally under salinity by 43.78 and 22.33%, respectively. Plants exhibited a significant suppression of shoot and root length which finally manifested in dry matter accumulation by 93.95 and 89.24%, respectively, for cv. Swarna and Swarna Sub1 under pre-treatment. Chlorophyll content significantly varied among the treatments as well as between the cultivars. Carotenoids and lycopene though depleted but had not any significant variation between the cultivars. NADP(H)-oxidase was distinctly overexpressed for cv. Swarna Sub1 by 1.16-fold under salinity than cv. Swarna (1.22-fold). Still, pre-treatment with silver has maximally induced superoxide content establishing oxidative sensitivities with a peak rise of 3.07 and 2.44-fold for two genotypes. Therefore, the significant traits linked to sub1A QTL would be the selection markers or to overexpress in susceptible genotypes under the condition of salinity for better sustenance.