Toss chopped tomato, red onion, jalapeño, cilantro, and lime juice in a bowl. Season with salt and set aside.
Pulse yellow onion, garlic, and remaining jalapeño in a food processor until finely chopped.
Brown ground beef in a skillet (6–8 min). Add onion mixture and taco seasoning; cook until it starts to stick (6–8 min). Add water and stir until sauce thickens (2 min).
Divide beef and cooked rice into bowls. Top with salsa, sliced avocado, tortilla chips, and shredded lettuce or cheese as desired. Serve.