Rinse and drain beans thoroughly then transfer to a large bowl and fill with cool water until beans are covered completely. Cover and soak at room temperature for 10-12 hours (or overnight).
Drain beans thoroughly and place in the bottom of a 6-quart slow cooker sprayed with nonstick cooking spray.
Add onion, dark brown sugar, molasses, apple cider vinegar, mustard, water, salt and pepper to the slow cooker; mix to combine.
Cover and cook on low for 6-8 hours or until the beans are tender. Season with additional salt and pepper as needed. Keep warm in slow cooker until serving.