Even though the tomatoes are turning black on their bottoms, blossom end rot does not spoil the entire fruit. It is fine to cut away the affected portion of a tomato and eat the rest. Your best bet for treating blossom end rot is to adjust your watering to make sure you are using good watering practices. this condition usually occurs when the fruit is half grown and can happen both when the fruit is green or has already begun to ripen. It begins with your tomatoes turning black at the bottom in a small area that seems water soaked and depressed. my tomatoes have black bottoms but why? Several factors can restrict a plants ability to absorb enough calcium for correct development. These include soil moisture variations (too wet, dry), soil nitrogen abundance, cultivational damage to the root, soil ph too high, soil ph too thin, salt cold, and high soil. End blossom rots are not a disease but a physiological problem arising from calcium deficiency in the tomato plants, leading to the formation of dark, brownish spots at the bottom of the fruit, where the blossom once was. some tomatoes turn black on the bottom due to blossom end rot, which is the result of a calcium deficiency during formation. This is most common in container gardening however, it can occur with any type of gardening. Calcium deficiency occurs due to inconsistent watering, too much wateringor fertilizing too much or too little. Tomatoes turning black on the bottom arent really rotten despite the name, blossom end rot is not a bacterial rot, nor is it a disease. It is a condition caused by a calcium deficiency experienced by the plant when the fruit is forming. Calcium is the nutrient necessary for forming the skin of the fruit.