Contestants compete through four rounds of competition until a final winner is chosen. The first round features 24 contestants (they were introduced from seasons 1–3, but from season 4 onwards, not all were shown) running through a series of obstacles. The top 12 finishing times move on. The show never made clear to viewers whether or how the finishing times are adjusted for failing to complete obstacles along the way.
The next two rounds take place on two different complex obstacles. They typically involve large structures that competitors have to enter, navigate around while hostile devices try to knock them off, and then jump to a landing pad to finish, where Jill Wagner awaits them. The competitors keep trying on these structures until roughly half of them have reached the finish; the other half are eliminated. This leaves only the top four (top three in some seasons) to make it to the final round called the Wipeout Zone, where the winner earns the title of Wipeout Champion and a $50,000 grand prize.
The challenges change each week, but always feature offbeat and comical obstacles, such as the "Sucker Punch", "Big Balls" (the show's trademark obstacle, four very large red spheres in sequence that must be traversed from a running start, with failures often resulting in odd-angle rejections), the "Sweeper", the "Dizzy Dummy" or the "Dreadmill". Emphasis is always placed on obstacles that can produce sudden jarring collisions (the obstacle surfaces are heavily padded and competitors sometimes don helmets or flak jackets) followed by spectacular falls into the water below, these being the show's titular "wipeouts". As part of wiping out, the competitors often end up covered in mud, froth, vats of food, or other unlikely substances.
In one of the show's trademarks, the commentators have a humorous running commentary, often mocking and insulting the contestants as they compete. The hosts make frequent use of puns. Jokey sound effects and cheesy visual effects are often added as well. The exchanges between the two hosts is often a subplot of episodes themselves, with Anderson playing it mostly straight as a play-by-play man while Henson offers up off-the-wall inanities and non sequiturs as color commentary. Jill Wagner offers additional features reactions, and also provides interviews with the contestants filmed before their turn begins. These interviews tend to emphasize bizarre aspects of contestants' personalities, with Wagner making facial commentary as the conversation proceeds. Generally only those who will pass the first round are introduced, and a nickname is assigned that is used throughout the game.
At night, the show takes an epic and serious turn, with the humor dialed down, and serious background music instead of its lighthearted theme music. The final four or three contestants play separately on a large obstacle course inside the studio called the Wipeout Zone, each attempting to finish the course in the fastest time, much like the first round. Though slight variations are used in each episode, contestants wear wetsuits and they begin by either sliding down a water ramp or being launched by a giant catapult or blob into the course, swimming to the first obstacle. Obstacles have varied between episodes, but the course contains several obstacles that must be traversed in order to reach the finishing platform. The player with the fastest time on the course is declared the "champion" of the episode and is awarded the show's grand prize of $50,000. The Wipeout Zone often brings competitors to the brink of exhaustion, especially when they have to swim back to a starting point to retry a failed obstacle. In Season 7, the Zone was all about speed, and the contestants were given 1 attempt per obstacle.