Team Wartortle debuted in The Pokémon Water War. While on Ascorbia Island, a fire broke out at an old warehouse. Ash and Misty had their Pokémon attempt to put the fire out, but it did little to stop the flames. When Team Wartortle arrived, they quickly put the fire out. However, the leader and Squirtle soon developed a rivalry. Squirtle wanted to prove to the head Wartortle that it was just as strong as its evolved form. It proved it when the leader and Squirtle worked together to save a little boy from a burning building. It seemed that after the rescue, the rivalry was settled.
However, it started back up again in The Fire-ing Squad!. During a Pokémon firefighting competition, Squirtle was reunited with not only Team Wartortle, but also its old friends from the Squirtle Squad. Team Wartortle believed they were going to be victorious in the competition, but once again Squirtle refused to be beaten by its evolved form. With its help, the Squirtle Squad won the competition.
Team Wartortle hasn't been heard from since Johto, and it is unknown what happened to them since then.