While Manuel was still a freshman at Stanford, she dealt with a variety of medical issues. She spent eight months with chronic sinusitis and a complete blockage of her right nostril. Then, just six weeks before the 2016 Olympic Trials, Manuel had balloon sinuplasty nasal surgery. However, she kept the surgery under wraps, as she didn't want anyone to think she was making excuses if she were to swim poorly. "So I was dealing with a lot of that pretty internally and still trying to make sure my goals were at the forefront," Manuel explained to NBC Sports in July 2020. Despite the surgery, she ended up placing second in the 50- and 100-meter freestyle, which qualified her to compete at the 2016 Summer Olympics.