Remove all of the blankets and sheets from the bed. Throw them into the laundry. Get some fresh bedding to put on the waterbed once it's clean.
Retrieve a damp washcloth. Rub the waterbed mattress from top to bottom in straight rows to remove any excess dirt or dust. Repeat this twice.
Fill a bowl with 2 cups of hot water and three capfuls of a disinfectant, such as Pine-Sol. The water should be steaming but not hot enough to scald your skin. Dip your second washcloth into the bowl mixture.
Wipe the waterbed mattress down. Use a circular motion to scrub the mattress. Start from the top of the bed and work your way down. Wring the washcloth out frequently. Repeat three times to clean the waterbed mattress properly.
Dry the mattress with your bath towel. Remove all the moisture from the waterbed before replacing the sheets and blankets. Start from the top and work your way down to the foot of the bed. Be sure you dry all the crevices as well.
Replace your bedding. Tuck in all the sheets and blankets. Place the pillows at the top of the bed under your blankets.