Mix the water, beans, and onion in a 4-quart Dutch oven. Cover and heat to boiling. Boil 2 minutes and remove from the heat; let stand for 1 hour. Add just enough water to the beans to cover. Stir in the remaining ingredients and heat to boiling. Cover and reduce the heat. Boil gently, stirring occasionally, until the beans are very tender, about 2 hours, (add water during the cooking time if necessary); drain the beans. Beans can be covered and refrigerated up to 10 days.