This training method is used to gain better chakra control. To do this, the user has to be emitting a constant stream of chakra from the bottom of their feet and using the repellent force to walk across the water's surface. This technique is more difficult to master than the Tree Climbing Practice, because the amount of chakra that needs to be emitted changes constantly.
It has also been shown that one can use their chakra to "skate" across the water surface, like an ice skater, instead of just walking or running. As Jiraiya noted, the more one trains this technique, the more they reach a state where they stand on water without even noticing it or basically even trying. Furthermore, this technique allows its users to walk on sticky surfaces without being affected.
It doesn't have to just be at the feet. A user under water can focus chakra on their hands or any other body part that makes contact with the water's surface. If they were submerged, they can climb atop the water as if they were climbing out of a pool.
- Naruto: Shippūden episode 14
- Naruto chapter 326, page 8