Bring a large pot of salted water to a boil. Add the spaghetti and cook according to package instructions until al dente, about 8-10 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium-high heat.
Add the ground beef to the skillet and cook, breaking it up with a spoon, until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
Add the chopped onion to the beef and cook until softened, about 4 minutes.
Stir in the minced garlic and cook for 1 minute until fragrant.
Add the crushed tomatoes, tomato paste, dried oregano, dried basil, salt, black pepper, red pepper flakes, and water to the skillet. Stir to combine.
Bring the sauce to a simmer, reduce the heat to low, and cook uncovered for 15 minutes, stirring occasionally.
Remove the sauce from heat and stir in the grated Parmesan cheese and chopped fresh parsley.
Divide the cooked spaghetti among four plates and spoon the beef tomato sauce evenly over the pasta.
Serve immediately with additional grated Parmesan cheese on the side.