Bauer began his career at the age of nine with TJ Škoda Ostrov, five years later he moved to LK Mattoni Karlsbad in 1991 , where Miroslav Petrásek was his coach. After triumphing in a national race for the first time in 1995, he became double Czech junior champion in 1996. In the same year the Czech competed for the first time at the Junior World Championships in Asiago , where he did not get beyond 17th place over 10 kilometers. In return, Bauer was able to place in the top ten in his first FIS races in the same year. When he again won the silver medal in the 30 km long distance in free style at the Junior World Championships in Canmore, Canada , he had his breakthrough. As a relay runner and starter on the 10-kilometer route, he was nominated for the Nordic World Ski Championships in Trondheim in 1997. While he was 47th out of 103 participants in the 10 km individual race of the classic technique, he even managed eighth place with the Czech relay. In the same year, the Czech association started Bauer for the first time in the cross-country skiing world cup of the 1997/98 season in Val di Fiemme . There he did not achieve any World Cup points in three races, thanks to his very successful starts at FIS races, where he came on the podium three times, he was nevertheless nominated for the 1998 Winter Olympics in Nagano . In three competitions he achieved a 32nd place in the pursuit as the best result, even over 30 kilometers he just missed the top 30 as 33rd.
After further successful FIS races and a victory in the Continental Cup , Bauer took part in the World Cup again at the end of 1998. On January 9, 1999, he reached in Nové Město na Moravě his first points in the highest competition series of the winter. Only shortly afterwards the Czech managed a surprising 13th place over 15 kilometers freestyle in Ramsau at the Nordic World Ski Championships , and he was also twentieth over 10 kilometers classic. In 1999 and 2000, Bauer won more points in the World Cup, and he also won an FIS race for the first time, where he also achieved podium places. His best individual World Cup result remained eleventh for some time, which he also achieved on his Czech home track in Nové Město. Although Bauer also performed well at the World Ski Championships in Lahti in 2001 and even finished fourth over 10 kilometers in a World Cup race at the beginning of the 2001/02 season in Kuopio , he only achieved the ultimate international breakthrough to the top of the world at the 2002 Olympic Games in Salt Lake City . Here he was among the top 10 three times, including a sixth place over 30 kilometers. Bauer had already achieved some single-digit results in the World Cup races before the Olympics, after which he achieved three top five results in the last six competitions of the season, with the relay he achieved his first podium position in third place.
The 2002/03 World Cup started like the previous one with some excellent results. Over the 15 km classic in Kuusamo , Bauer came second, and in January 2003 he won his first World Cup race again in Nové Město. He ended the season with four triumphs in a row in the lower class FIS races, all over 10 kilometers. In the 2003/04 and 2004/05 seasons there were further podium finishes and two victories, this time in Lahti and Pragelato , but he was also without a medal at the 2005 World Ski Championships in Oberstdorf . Bauer ended this series of failing to achieve a medal at major events at the 2006 Olympic Games in Turin , where he won silver over 15 km classic. After remaining without an individual podium in the 2006/07 World Cup , the 2007/08 season became his most successful to date. Bauer triumphed in two World Cups in 2007 , and Bauer dominated the Tour de Ski 2007/2008 , which was held for the second time , and won by almost three minutes. Another four World Cup victories followed in 2008, so that Bauer was able to win the overall World Cup with a clear 600-point lead over René Sommerfeldt . He also won the Distance World Cup.
At the beginning of the 2008/09 season , Bauer achieved second place over 15 km classic in Kuusamo . He finished the Tour de Ski 2008/09 in tenth place. At the following World Cup in Otepää , he won over 15 km classic. At his home World Championship in Liberec , he won the silver medal in the 15 km classic. In March 2009 he became the Czech champion over 10 km and 15 km. At the World Cup finals in Falun , he finished 12th overall and thus reached ninth place in the overall World Cup and fifth place in the Distance World Cup. In the 2009/10 season he won the Tour de Ski for the second time . This was followed by a victory in Otepää over 15 km classic and a second place in Lahti in the 30 km pursuit race. At the 2010 Olympic Games in Vancouver , he won the bronze medal with the relay and over 15 km freestyle. At the end of the season he came ninth in the World Cup finals in Falun and finished second in the overall and distance World Cups. In March 2010, as in the previous year, he became Czech champion over 15 km. In the 2010/11 season he came ninth at the Nordic Opening in Kuusamo and third at the 2010/11 Tour de Ski . At the World Cup in Davos , he came third over 15 km classic. At the Nordic World Ski Championships in Oslo in 2011 , he finished 13th in the 50 km mass start race, eighth place with the relay and seventh place over 15 km classic. At the end of the season, he achieved seventh place in the World Cup finals, fourth place in the overall World Cup and third place in the Distance World Cup.
In the following season, Bauer finished ninth at the Nordic Opening and sixth at the Tour de Ski 2011/12 . At the World Cup in Otepää he came second over 15 km classic and in Davos third place over 30 km freestyle. He finished the season in the overall and distance World Cup in 13th place. At the beginning of the 2012/13 season he came 24th at the Nordic Opening. The Tour de Ski 2012/13 he finished as last year to sixth place. At the World Cup in La Clusaz he reached third place with the relay. His best placings at the Nordic World Ski Championships 2013 in Val di Fiemme were 16th in the 50 km mass start race and 11th in the relay. At the World Cup final in Falun he came in 22nd place and reached 12th place in the overall World Cup. At the beginning of the 2013/14 season he came 11th at the Nordic Opening in Kuusamo . He won the stage over 10 km classic. At the 2014 Olympic Games in Sochi , he finished 31st in the 50 km mass start race, eighth place with the relay and fifth place over 15 km classic. At the World Cup finals, he came in 13th place overall and finished the season in 20th place in the overall World Cup and tenth place in the Distance World Cup. In the 2014/15 season he reached 32nd place at the Nordic Opening in Lillehammer . At the 2015 Nordic World Ski Championships in Falun, he won the silver medal in the 50 km mass start race.
Bauer lives in Boží Dar (Gottesgab) and has been training with the German athletes in neighboring Oberwiesenthal since 2006. He has also been taking part in the DSV courses since then. He is married to Kateřina (sister of Helena Erbenová ) and has two children.