As a senior, he broke his fibula and tore ligaments in his ankle, but still managed to record 38 tackles, two interceptions and four pass break-ups, earning first-team All-state and All-region selections by the Wisconsin Football Coaches Association.

In baseball, Waynes earned first-team All-county honors as an outfielder as a junior in 2010 after leading the Red Devils in home runs (3) and finishing second in batting average (.452, 28-of-62).

In 2011, he finished third in the 100m (10.85 s) at the Division I State T&F Championships,[5] and recorded a career-best time of 10.75 seconds in the 100-meter dash at the SEC Outdoor Conference Meet, where he placed first.

He was redshirted as a true freshman in 2011 after suffering a season-ending injury when he broke his fibula and tore ligaments in his knee as a senior in high school.

In the 2012 Buffalo Wild Wings Bowl game against TCU, he played a majority of the snaps at cornerback and tallied a season-high three tackles; he was also credited with a half sack for a loss of 1 yard against the Horned Frogs.

As a redshirt sophomore in 2013, Waynes started all 14 games at field cornerback for the Spartans, recording a career-high 50 tackles (1.5 for loss), five pass deflections and three interceptions.

5 Stanford, he recorded his third interception of the season and tallied three tackles, helping Michigan State win their first Rose Bowl since 1988.

In Waynes's final game as a Spartan, he registered three tackles and a pass break-up in the Cotton Bowl Classic win over #4 Baylor.

[20] Throughout training camp, Waynes competed against Captain Munnerlyn, Terence Newman, and Josh Robinson to be a starting cornerback.

[21] Head coach Mike Zimmer named Waynes the fourth cornerback on the depth chart to begin the regular season, behind Xavier Rhodes, Newman, and Munnerlyn.

[23] On December 10, 2015, Waynes earned his first career start as a nickelback after Terence Newman was moved to safety due to multiple injuries.

Waynes was thrust into a pivotal pass defense role during the second half after veteran cornerback Terence Newman suffered an ankle injury.

Five plays later on a fourth-and-three situation, Waynes intercepted Wilson at the Vikings' 22-yard line after the ball was tipped by a Seahawks' tight end.

[26] Zimmer named Waynes the third cornerback on the depth chart to start the regular season, behind Rhodes and Terence Newman.

The following week, Waynes was moved to nickelback and replaced at outside cornerback by Alexander after drawing consecutive penalties in the third quarter and struggling to cover wide receiver Jordy Nelson.

Waynes finished the Vikings' 17–14 win against the Green Bay Packers with four solo tackles, one pass deflection, and an interception.

[29] On December 11, 2016, Waynes recorded one tackle and broke up a pass before exiting in the third quarter of the Vikings' 25–16 win at the Jacksonville Jaguars due to a concussion.

On January 14, 2018, Waynes started his first career playoff game and recorded four solo tackles and broke up one pass during a 29–24 win against the New Orleans Saints in the NFC Divisional Round.

The following week, he made three combined tackles and broke up a pass as the Vikings were eliminated from the playoffs after a 38–7 loss at the Philadelphia Eagles in the NFC Championship Game.

[38] Defensive coordinator George Edwards retained Waynes and Rhodes as the starting cornerback tandem entering training camp.

Zimmer officially named Waynes and Rhodes the starters to begin the regular season, alongside safeties Harrison Smith and Andrew Sendejo.

[49] Waynes remained on the roster and active throughout the Bengals' playoff run and in Super Bowl LVI, though only playing very few select special teams snaps.