At the NCAA championships she placed 5th in the 200 back in an all-time Big 12 record of 1:54.09. She also placed 13th in the 200 free and 14th in the 500 free becoming the first swimmer in Texas A&M history to swim in three individual evening finals at a NCAA Championship. In the summer before her junior year, Kristen took fifth at summer nationals in the 200 back and qualified to be part of the U.S. National Team that participated at the Japan International Grand Prix in Japan. Kristen was part of the Texas A&M's team which placed 4th at the NCAA Championships at Ohio State University. At the 2008 NCAA Championships, Heiss placed 3rd in both the 200 backstroke (1:53.37) and the 500 freestyle (4:40.03). She swam the second leg of the Aggies' NCAA runner-up 800 freestyle relay that swam the 3rd fastest time in NCAA history (6:59.50). Successfully defended her title in the 200 backstroke at the 2008 Big 12 Conference championship. At the 2008 United States Olympic Trials, she finished 5th place in the 200 meter backstroke in a time of 2:10.18. Throughout the 2008 Trials, Heiss kept a blog about her experiences and the trials, and will serve as an editorial intern for Swimmingworldmagazine.com. Her performance, including her three career-best 200 Backstroke times, and two career-best 200 freestyle times, came less than two weeks after spending 5 days in a Bryan, Texas hospital undergoing treatment for pulmonary embolisms. At the 2008 Swimming US Open, Heiss finished second to world record holder Hayley McGregory in the 200 meter backstroke under the meet record set by Olympian Margaret Hoelzer with a time of 2:09.99. With this performance, she secured a spot on the 2009 World University Games in Belgrade, Serbia. The next night, she took silver in the 400 meter freestyle with a time of 4:09.25. On the third night, Heiss took gold in the 200 freestyle, being only the 2nd A&M swimmer to ever do so. She tied with former NCAA Champion Mary Descenza in a lifetime best of 1:59.43. Heiss Redshirted the 2008–2009 collegiate season while recovering from shoulder surgery. Seven months after shoulder surgery, Heiss returned to the pool in July 2009 to compete in the World University Games in Belgrade, Serbia.