The objective of this study was to examine responses of vegetable seedlings grown on plug seedling system (Plug) or cylindrical paper pot (CPP) system to water stress. Cucumber 'Jo-eun' was grafted onto stock 'Huckjong'. Watermelon 'Jo-eunggul' was grafted onto stock 'Bulojangsaeng'. Growth factors of seedlings were investigated. Top-to-root ratio (TRR), compactness (CP), and Dickson Quality Index (DQI) as indicators of seedling quality were calculated based on time periods. Results revealed that the overall shoot of cucumber and watermelon grown in the CPP system was higher than the shoot grown in the Plug system. In both CPP and Plug systems, the total growth decreased as the irrigation water volume increased, while the seedling stem was thick and hard. The higher the irrigation water level, the greater was the inhibition of root zone development. When the degree of growth reduction was comparing between the two systems, the growth rate of cucumber was lower in the CPP system than that in the Plug system, whereas the growth rate of watermelon was decreased due to increased irrigation water content only in the Plug system. The degree of growth tended to decrease with increasing volume of irrigation water in both CPP and Plug systems. The degree of decreased growth was greater in the Plug system than in the CPP system. The decrease started to occur in the mid-growth phase. It intensified with further growth. In conclusion, extensive irrigation during early stages of growth can enhance the growth of seedlings in both CPP and plug systems. However, growth was suppressed after reaching a certain level. This effect was relatively lower in the CPP system than in the Plug system.