McMahon took over the head coaching position at Florida in June of 2001 and compiled a record of 231-143-1 (.617) during his six seasons directing the Gators. Florida advanced to the NCAA Tournament in four of six years under his guidance and finished as the runner-up at the 2005 College World Series. During his tenure, UF claimed the first two Super Regional berths in school history, a pair of Regional Championships and one SEC crown.
In 2005, McMahon was named the College Baseball Foundation National Coach of the Year, ABCA South Region of the Year and the SEC Coach of the Year. There were 61 Academic All-SEC selections at Florida over his first five seasons (the 2007 recipients have yet to be released) and 31 Major League Baseball Draft choices, including recent first-round pick Matt LaPorta.
McMahon arrived at Florida after serving for four years as the head coach at SEC Western Division rival Mississippi State. While manning the bench in Starkville, he directed the Bulldogs to a College World Series appearance in 1998, consecutive NCAA Super Regional berths when the format changed in 2000 and 2001 and four-straight NCAA Regional berths. In 2001, the Maroon and White claimed its first SEC Tournament title since 1990 and reached NCAA Super Regional play for the second season in a row en route to a 39-24 mark.
From 1983-89, he served as an assistant for Ron Polk, helping the Bulldogs scale new heights on the diamond. During that seven-year stretch, Mississippi State enjoyed some of its more memorable moments, claiming six NCAA Regional berths and securing three College World Series appearances while hosting five Regionals at Dudy Noble Field. MSU's powerful 1985 squad, featuring eventual Major League standouts Jeff Brantley, Will Clark, Rafael Palmeiro and Bobby Thigpen, proved to be one of the most accomplished teams in college baseball history. The 'Dogs posted their first-ever 50-plus win season (50-15) en route to a tie for third place at the College World Series. The 1989 team bettered that mark with a 54-14 finish, the school‚s 10th SEC baseball crown and a runner-up performance in the NCAA South Regional.
McMahon guided Old Dominion to newfound prominence and levels of success between 1990-94, including two NCAA Regional appearances, a pair of school-record 40-plus win seasons and an outstanding 189-86 (.687) record. During his first season as a collegiate head coach, McMahon was voted both the Sun Belt Conference and state of Virginia Coach of the Year in 1990 after piloting ODU to only its second NCAA Regional appearance. His 1994 edition sported a 40-14 overall mark, seized the Colonial Athletic Association regular-season title and advanced to the NCAAs. For his efforts, he was honored as the Coach of the Year by both the CAA and the state of Virginia.