Heat the oven to 375°F and add the dry ziti to a 9-by-13-inch baking dish.
Pour in the marinara and water, season with the salt and black pepper, and stir until the pasta lies mostly below the liquid.
Drop the ricotta in tablespoon-size pockets across the dish without blending them into the sauce.
Cover tightly with foil and bake for 45 minutes, until the ziti is nearly tender.
Remove the foil, stir once around the ricotta pockets, and cover the top with mozzarella.
Bake uncovered for 12 to 15 minutes more, until bubbling and browned, then rest for 10 minutes.