Preheat the oven to 325°F (163°C) and lightly grease a Dutch oven or baking dish.
In a skillet over medium heat, cook the chopped bacon until it becomes lightly crisp and releases its fat.
Add the chopped onion to the bacon and sauté for 3–4 minutes until the onion turns soft and translucent.
In a mixing bowl, whisk together molasses, brown sugar, ketchup, mustard, salt, pepper, and water until the sauce looks smooth.
Place the cooked navy beans in the Dutch oven and stir in the bacon-onion mixture.
Pour the prepared sauce over the beans and gently stir until everything is evenly coated.
Cover and bake for about 1½ to 2 hours, stirring once halfway through, until the sauce thickens and the beans look glossy.
Remove from the oven and let the beans rest for 10 minutes so the sauce settles and becomes richer.