Stir water and half the pizza sauce together in the bottom of a 13x9-inch baking dish. Lie spaghetti atop the sauce mixture. Arrange chicken atop the noodles.
Pour remaining sauce over the chicken breasts and spaghetti; top with pepperoni and mozzarella cheese. Cover the baking dish with aluminum foil.
Bake in preheated oven for 45 minutes.
Remove foil and continue baking until chicken is no longer pink in the center and cheese is bubbling, 5 to 10 minutes more. An instant-read thermometer inserted into the center should read at least 165 degrees F (74 degrees C).
