The 2000 season started off in typical fashion for Wagner, who saved three of the Astros' first four wins while retiring 16 of the first 20 batters he faced. However, after recording a save on May 4 against the Chicago Cubs, he suffered back-to-back blown saves on May 12–13 against the Reds. While he was still occasionally throwing 100 m.p.h. as measured by radar, he was not throwing his slider at 85 to 90 m.p.h. as often as he had been previously. Wagner continued to struggle before going on the disabled list with a torn flexor tendon in his pitching arm and would miss the final three and a half months of the season. He finished with a 2–4 record, a 6.18 ERA, and six saves in 15 opportunities, striking out 28 and walking 18 in innings. He would rebound in 2001. Coming off elbow surgery, he posted a record of 2–5 with 39 saves in 41 chances and an ERA of 2.73. He was one of the leading candidates for The Sporting News Comeback Player of the Year Award in the National League. In innings, he struck out 79 hitters.