Preheat the oven to 350 degrees F. Brown the ground beef and onion in a large skillet over medium-high heat while breaking up into chunks with a spatula until cooked through and no longer pink. Drain fat.
Season with salt and pepper and taco seasoning. Add salsa, chiles, and water. Bring to a boil, then reduce heat to low, cover and simmer for 5 minutes.
Remove from heat and stir in rice, 1 cup of shredded cheese, and refried beans. Transfer the mixture to a 9×13 inch baking dish.
Place into the oven and bake for 30-35 minutes or until the dish is warmed through. During the last few minutes of cooking, top the dish with shredded cheese and tortilla chips. Cook until the cheese has melted.