Add pasta, pizza sauce and water to the slow cooker. Stir well. Cook on low and cover.
Stir after 60 minutes. Add ⅔ cup cheese and ⅓ cup quartered pepperoni. Top with remaining 1 ⅓ cup shredded cheese and pepperoni rounds. Replace cover.
Cook on low for an additional 60 minutes. The total cook time is 2 hours. Slow cookers can run warmer and I advise to check the pasta at the 90 minute mark.