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Over-watering sunflowers canOver-watering sunflowers can sometimes cause deformed seed heads. But it sounds more like a disease or an insect problem. Sunflower seed maggots can get into the buds and deform the flowers. Check your flowers for bug activity. Aster yellows is a disease that is spread by six-spotted leafhoppers and can result in misshapen heads and petal formation. Try crop rotation next year by planting your sunflower seeds in a different spot in your garden where you haven't grown them before.