Sunflower (Helianthus annuus L.), which is widely grown globally for its high-quality edible oil, is reasonably salt and drought tolerant but it is susceptible to waterlogging. In the saline coastal zone of the Ganges delta, sunflower is often exposed to sudden heavy rainfall during early growth but plant tolerance to such events is not known. Hence, we evaluated the effect of short-term soil inundation (referred to as waterlogging) for 0, 24, 48 and 72 h on sunflower at emergence, 2-leaf, and 4-leaf stages in early- and late-sown crops under field conditions (saline, clay-textured soil, and shallow groundwater). Waterlogging for 24 h did not affect sunflower at any stage but waterlogging for 48 and 72 h suppressed emergence and growth at the 2 and 4-leaf stages. Waterlogging for 72 h completely prevented the emergence for early sowing, whereas emergence was less affected for later sowing. Shoot and root dry weight were most affected at the emergence and 2-leaf stage, not at the 4-leaf stage. In conclusion, waterlogging caused by more than 24 h soil inundation at up to the 4-leaf stage severely depressed emergence and growth, indicating the need for effective drainage at sowing of sunflower in the low-lying coastal saline zone of Bangladesh.