After failing to win the competition, Nowinski made appearances in independent promotions in Massachusetts before being hired by WWF and entering its developmental territories.

[10] Nowinski made his first major independent appearance in London, UK for the Frontier Wrestling Alliance promotion at its Lights Camera Action show on December 14, 2001.

On the June 10, 2002, episode of Raw, Nowinski debuted in WWE as a heel, helping William Regal beat Bradshaw in a European Championship match.

Over the next few weeks, Nowinski claimed victories over Jeff Hardy and Booker T before starting a feud with his former Tough Enough trainer, Al Snow.

The feud come to an end on the May 12 episode of Raw, where Nowinski teamed with La Résistance (René Duprée and Sylvain Grenier) in a losing effort against Steiner, Test and Goldust.

On the May 26 episode of Raw, Nowinski aligned himself with Thuggin' And Buggin' Enterprises, an African American wrestling stable consisting of Rodney Mack, Jazz and their manager Theodore Long.

Nowinski wrestled his final televised match, due to him sustaining post-concussion syndrome, on the June 23 episode of Raw, in a losing effort against Maven.

His last match was on July 12 with Rodney Mack defeating Rosey and Tommy Dreamer at a house show in Green Bay, Wisconsin.

Bennet Omalu, a pathologist at the University of Pittsburgh announced that "the condition of Waters' brain tissue was what would be expected in an 85-year-old man, and there were characteristics of someone being in the early stages of Alzheimer's".

[22][23] Nowinski played a role in the discovery of the fourth case of chronic traumatic encephalopathy (CTE) in a former NFL football player, former Pittsburgh Steelers offensive lineman Justin Strzelczyk, who was killed in an automobile crash in 2004 at age 36.

[8] On June 14, 2007, Nowinski and Robert Cantu founded the Concussion Legacy Foundation (CLF) in Boston, Massachusetts in reaction to medical research indicating brain trauma in sports had become a public health crisis.

The initial vision of the CLF was to formalize neuropathological research and develop and treatment, via partnership with a top-tier university medical school.

[30] CLF has sought to develop ways to raise awareness of the issue and to directly educate coaches, athletes and parents and has been featured in articles in The New York Times,[31] on news programs such as 60 Minutes[32] and Frontline,[33] and CNN.

[34] In August 2010, Nowinski took offense to Linda McMahon saying during her Senate campaign that she only met recently overdosed wrestler Lance Cade "once" and said it was "absolutely unsafe to work in that ring.

[37] In January 2023, Nowinski presented warnings and criticism of an increased prevalence in slap fighting, to include a U.S. based reality show focused on the emerging sport.