Heat olive oil in a large skillet over medium heat.
Add chopped onion and cook for 3-4 minutes until softened.
Add minced garlic and cook for 1 minute until fragrant.
Add ground beef to the skillet and cook, breaking it apart with a spoon, until browned and cooked through, about 6-8 minutes.
Drain excess fat from the skillet if necessary.
Stir in marinara sauce, water, uncooked penne pasta, dried Italian seasoning, salt, and black pepper.
Bring the mixture to a boil, then reduce heat to low and cover the skillet.
Simmer for 15 minutes, stirring occasionally, until the pasta is tender and most of the liquid is absorbed.
Remove the skillet from heat and gently stir in the cottage cheese.
Sprinkle shredded mozzarella and grated Parmesan evenly over the top.
Cover the skillet again and let it sit for 5 minutes to allow the cheeses to melt.
Garnish with chopped fresh basil before serving.