Flippers allow Chip to swim through water safely if he is unable to use blocks to do so, or if for time reasons this is a faster way over. Flippers do not, however, protect him from any gliders that may be swimming with him.
As with all other boots, it is taken away when Chip lands on a thief, and is an acting wall to monsters only. Chip can collect flippers touched by a block by simply pushing the block again.
In Lynx, instead of flippers, a "water shield" is used, as seen by the different hint in Lesson 3.