Heat oil in a large saucepan over medium heat. Add onion and cook until soft, 3 to 4 minutes. Add sausage; stir to break up lumps and cook until lightly browned and crumbly, 6 to 8 minutes. Drain and discard grease.

Add undrained tomatoes, water, basil, oregano, and parsley to the pan; bring to a boil over medium heat. Reduce heat to low and cook, partially covered, for 25 minutes.

Meanwhile, bring a large pot of lightly salted water to a boil. Cook rigatoni in the boiling water, stirring occasionally until tender yet firm to the bite, 10 to 12 minutes. Drain, rinse under cool water, and drain again. Transfer to a large bowl and set aside.

Preheat the oven to 350 degrees F (175 degrees C).

Uncover the sauce and increase heat to medium. Cook, stirring occasionally, until sauce thickens, 6 to 8 minutes. Remove from heat and add 2/3 of the sauce to pasta; toss to combine. Stir in mozzarella cheese and 1 cup Parmesan cheese. Transfer to a 9x13-inch baking dish, pour remaining sauce over top, and cover with aluminum foil.