The night before, combine the Great Northern Beans and water in a large saucepan. Bring to a boil, and cook for 1 1/2 hours. Pour beans and their liquid into a bowl, cover and refrigerate overnight.
In the morning, drain off liquid, reserving 1 cup. Pour beans and the reserved liquid into the crock of a slow cooker. Stir in the salt pork, onion, molasses, brown sugar, mustard and pepper. Cover, and cook on Low for 12 to 14 hours. Stir before serving.