Cook the quinoa and water according to the package directions, and set aside.
Preheat the oven to 375 degrees. Grease a 2 quart baking dish.
In a large bowl, combine the cooked quinoa, green chilies, salsa, black beans, corn, cumin, chili powder, salt and pepper. Stir in the Monterey jack cheese.
Pour the quinoa mixture in to the prepared baking dish. Top with the Colby jack cheese.
Place the dish in the oven and bake for 20 minutes, or until the casserole is heated through and the cheese on top has melted.