Place the navy beans into a large container and cover with several inches of cool water; let stand 8 hours to overnight. Drain and transfer beans to a pot; add enough water to cover beans.
Bring water to a boil, reduce heat, cover pot, and simmer until beans are slightly tender, about 1 hour.
Mix 4 cups water, molasses, brown sugar, salt, mustard, and pepper together in a bowl until smooth.
Mix beans, salt pork, and onion together in a slow cooker. Add molasses mixture and more water to cover beans if needed; stir well.
Cook on Low for 8 to 10 hours.
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