Because the boys are visiting a water park/pool and it would be very odd to have Kenny keep his hood on, Kenny appears with his hood off, but his face is always obscured either by him being turned away from the camera or having another character block the view of his face.
During one of the final scenes, an alien holding a banana is visible among the crowd in the background. The alien was placed in the episode as part of a contest offered by the show's official website, in which viewers who could find and identify the alien in the episode could enter a contest, with the winner getting an animated version of himself or herself placed in the South Park opening credits.
"Pee" served as a parody of the disaster film genre, particularly the movie 2012 which was released five days before "Pee" was broadcast.
There is also a reference to the film Alive (1993) when Randy comes to rescue the children on a helicopter. He is holding a red baby shoe, just as Nando Parrado at the end of the movie.