Brown ground beef in a medium skillet on medium heat with onion and jalapeño pepper; (if hamburger has high fat content, drain excess fat before proceeding).
Stir in water and taco seasoning; bring to a bubbly boil; reduce heat to low and simmer (uncovered) until liquid is reduced by half or more.
Stir in lime juice, black and refried beans.
Preheat oven to 425°F; line a deep baking dish with aluminum foil, or coat with non-stick cooking spray.
Lay half the tortilla chips in a single layer in a the baking dish; spoon half of the meat and bean mixture on top of the chips; sprinkle half the cheese on top of this; rRepeat with the other half of each.
Bake 15 minutes; serve with a toppings bar, or top the entire pan and serve.