In a large pot or deep skillet, heat the olive oil over medium heat.
Add the chopped onion and sauté for 3-4 minutes until translucent.
Add the minced garlic and cook for another 1 minute until fragrant.
Pour in the diced tomatoes with their juice, water, dried oregano, dried basil, red pepper flakes, salt, and black pepper. Stir to combine.
Add the dried penne pasta to the pot and stir to submerge the pasta in the liquid.
Bring the mixture to a boil, then reduce heat to medium-low and simmer uncovered for 12-15 minutes, stirring occasionally, until the pasta is cooked and most of the liquid is absorbed.
Once the pasta is tender, gently fold in the drained tuna, breaking it up slightly with a spoon.
Cook for an additional 2 minutes to heat the tuna through.
Remove the pot from heat and stir in the grated Parmesan cheese and chopped fresh parsley.
Serve immediately, garnished with extra Parmesan and parsley if desired.