Cut each squash in half and scoop out the fibers and seeds.
Place the squash halves, cut-side down, in a baking dish. Pour the water around the squash and cover the dish closely with aluminum foil. Bake for about 40 minutes or until squash is tender. To test for doneness, insert a fork or knife inside the squash flesh.
When tender, turn the squash cut-side up. Sprinkle with salt. Add equal portions of butter, brown sugar, and nutmeg to the center of each squash half and bake uncovered until the sugar melts.