After playing youth football for two clubs, Nowotny finished his formation with Karlsruher SC. He made his first team – and Bundesliga – on 2 May 1992, playing the entire 1–0 away win against Hamburger SV, and finished the season in the starting eleven, as the club collected three wins in four matches and finished in eighth position. Still not in his 20s, Nowotny became a defensive mainstay for Karlsruhe. On 10 April 1993, he scored a brace for the club in only ten minutes, in a 2–2 draw at VfL Bochum, and went on to collect nearly 150 official appearances during his spell, including four in the 1993–94 UEFA Cup. Aged 22, Nowotny signed for Bayer 04 Leverkusen, making his league debut on 21 August 1996, a 3–1 away success against MSV Duisburg. An undisputed first-choice from the start, he appeared in 32 matches in his first season, as the club finished in second place, trailing FC Bayern Munich by two points; he continued to appear regularly during his stay, often forming an efficient defensive partnership with Carsten Ramelow. On 30 October 1998, Nowotny scored his first league goal for Leverkusen, in an 8–2 home demolition of Borussia Mönchengladbach. Additionally, he appeared in 16 games in the club's 2001–02 UEFA Champions League runner-up run; however, he was greatly missed in the following season's league campaign, only appearing once as the club finished in 15th position, narrowly escaping relegation, and having the fourth-worse defensive record in the league, at 56 goals conceded. On 28 September2004, Nowotny scored his first and only Champions League goal, in Bayer's 2–4 away defeat against FC Dynamo Kyiv. He left the club in the 2006 summer, with more than 300 official appearances - 231 in the Bundesliga - in 10 years.
Abroad spell
On 18 July 2006, 32-year-old Nowotny agreed to sign a three-year contract with Croatian LeaguechampionsNK Dinamo Zagreb. He made his debut for Dinamo on 29 July, against NK Slaven Belupo, in the first domestic league match of 2006–07, and also appeared in the club's Champions League qualifying round against Arsenal – the English had tried to sign him in the past – a 0–3 home defeat. On 19 August 2006, Nowotny suffered an injury during Dinamo's home match against NK Međimurje, a 4–1 win. Even though he was not fully healed and had played all 90 minutes for Germany in a friendly match only three days earlier, he asked to play because his wife and children came to Zagreb to watch him. Coach Josip Kuže, as he later admitted, had his doubts about the player's decision to play; he also had thoughts to substitute him by the end of the match, but changed his mind because of the fans, who had accepted Nowotny with acclamation. After the match, his injury became more serious, and needed surgery, and a one-month layoff. Eventually, on 22 January 2007, Nowotny announced his retirement from football, not being able to fully recover. He said: "To think I may have to wait another 10 months through physiotherapy and returning to training – this is enough.", said the 33-year-old.
