Reserve about ¼ cup of the diced onion and place in a small bowl. Add the cilantro, tomato, and jalapeño. Stir and set aside.
Heat a large oven proof skillet over medium-high heat. Add the ground beef and the rest of the onion. Cook, breaking up the beef with a spatula, until the beef is browned and the onions are soft, 5-7 minutes. Drain any excess fat from the pan. Sprinkle the taco seasoning over the beef mixture, add the water, and stir. Add the tomatoes and beans and cook, stirring occasionally, until heated through, about 3 minutes. Gently stir in the tortilla chips.
Preheat the broiler to high and place the top rack about 6 inches from the heat source.
Sprinkle the cheese over the top and broil until the cheese is melted, about 2 minutes. Sprinkle the onion cilantro mixture over the top and serve.