Biochemical and physiological processes serve as key indicators for assessing the adverse effects of biotic and abiotic stressors in plants. Due to the limited and incomplete information on the growth, root morphology, and physiology of watermelon lines under cold stress in Korea, this study aimed to evaluate selected cold-tolerant lines (PI254744, SW20, and SW66) and cold-sensitive lines (PI525233 and SW54). The evaluation was based on root and shoot weight, root and shoot length, root morphology, photosynthetic pigments (chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids), and levels of proline, malondialdehyde (MDA), and soluble sugars in root and leaf samples collected at various time points. Two treatments were conducted: one at 28 °C as a control and one at 10 °C to simulate cold stress. The results revealed a decline in growth variables under cold stress compared to the control across all lines. However, the disintegration of root cellular structures and reduction in growth variables were less severe in the tolerant watermelon lines than in the sensitive ones. Under cold stress, proline, MDA, and soluble sugar levels increased in all watermelon lines relative to the control. Notably, the tolerant lines displayed elevated proline and soluble sugar levels, while the sensitive lines had higher MDA content. Furthermore, photosynthetic pigment levels were generally lower in all lines during cold treatment compared to the control, though the reduction was less pronounced in the tolerant lines than in the sensitive ones. A significant positive correlation was found between the percentage reduction in total chlorophyll content and the percentage reduction in growth variables. The lesser reduction in photosynthetic pigments, combined with higher levels of osmoprotectants (proline and soluble sugars) and lower MDA levels in the tolerant lines during cold stress, may suggest underlying mechanisms that warrant further biochemical and molecular studies to better understand cold resistance.