This study evaluated not only the seedling performance of two tomato varieties (Marmande and Kecskeméti Jubelium) under irrigation with nutrient-deficient water and drought stress but also salicylic acid application on alleviating seed-borne disease of tomato caused by Alternaria alternata. Results indicated that The outcome indicated that the Kecskeméti Jubileum demonstrated a higher degree of growth in certain environmental parameters, although both Kecskeméti Jubileum and Marmande cultivars can germinate in the condition of nutrient-deficient water. Nevertheless, when applying levels of drought, the Marmande variety had a higher viability rate of 62.5% in comparison with another variety, and the germination rate of the two tomato varieties is at 85.5% in 5% but decreased progressively when exposed to a higher drought concentration of 10%. When using 3 ml of salicylic acid during germination stages, the seedling vigor index of Marmande shows a greater index at 165 in comparison to Kecskeméti Jubelium just 108 under the infection of Alternaria alternata.