Place beans in 6 cups of water. Bring to boil; turn heat down and simmer while preparing vegetables.
Peel and dice squash, add to soup pot along with additional 4 cups of water and continue to simmer for 1 hour.
In a separate skillet, sauté the onions, celery, fennel and garlic till tender. Add to the soup pot along with the ginger and nutmeg and seasonings. Simmer for 15 minutes uncovered.
You made add more water or vegetable broth to adjust the consistency of the soup. Also, if you like, you can purée half of the soup mixture for a creamy consistency.