Preheat oven to 375°F. Coat a 9-inch square or a 10x8" pan with cooking spray.
Combine the almonds, walnuts, onion, garlic, basil, nutmeg, salt, pepper and water in a food processor and process until smooth, about 1 minute.
Spread 1/2 cup of the marinara sauce on the bottom of the pan. Cover with half of the uncooked noodles, spinach, tomatoes and nut mixture. Repeat the layers again and transfer to oven. Bake for 50 minutes, until lightly browned.