Place the water in a large pan with the onion, green pepper, and garlic. Cook over medium heat, stirring frequently, until softened, about 5 minutes. Add the beans, corn, rice, tomato sauce, chilies, chili powder, and cumin. Stir to mix, then cook over low heat until warmed through, about 10 minutes. Remove from the heat and set aside.
Preheat the oven to 350º. Pour about 1/2 cup of the enchilada sauce into the bottom of a 13 x 9-inch casserole dish and spread evenly over the bottom. Pour the rest of the enchilada sauce into a bowl. Dip 4 of the tortillas, one at a time, into the enchilada sauce, then layer them in the bottom of the casserole dish.
Spread half of the bean mixture over the tortillas. Repeat with the next 4 tortillas and the remaining mixture. Finish with the last 4 tortillas. Pour the remaining enchilada sauce over the top and spread evenly. Sprinkle with the chopped green onion.
Cover and bake for 40 minutes. Remove from the oven and let rest 5 minutes before serving. Serve with salsa to spoon over the top, if desired.