Perhaps the least fun part of your Grand Canyon rafting trip will be getting used to the necessary routine of packing out your own waste and toilet paper. Unlike many other wilderness areas, where you can simply bury feces, the NPS forbids this in the Grand Canyon National Park. The area sees so many visitors each year that the area won't be able to naturally decompose everyone's waste. The waste can in turn contaminate the water and land, becoming a danger to future visitors and wildlife.
It would be best to purchase a handy portable toilet system that allows you to deposit the waste directly into a container. These systems must be washable and reusable, and allow you to safely transfer the waste to sewage treatment facilities after your trip is over. As an alternative (such as in between camps or on a day hike), you should bring a toilet system that uses special chemicals to treat waste, making it safe for landfills. Store bags of waste in a waterproof container.
To be sanitary, you should wear rubber gloves when setting up and breaking down the toilet system at your campsite. Disinfect these gloves after use, and use a disinfectant on the toilet seat. Keep soap handy at the toilet system for each camper to use when he or she is done.
Although you have to be careful to carry out all feces, it is, however, permissible to urinate in the river. The NPS asks visitors to urinate directly into the river and not on the beaches, as the sandy beaches don't have enough organic material to process the urine. Even hitting the wet sand near the water can leave a nasty, green algae.