After getting inside the sewer of South Park, I used alien probe to cross the gap. And then climbed down the stairs. Now I can see a water flowing down. There is a valve above it. How do i reach it?
To get through the sewer flow, you'll see the valve above it twinkeling a little. When they do that you can shoot at it.
Shoot at the valve.
Edit: As Eric Tobias said there are 2 kinds of valves, the ones on top of the pipes which you can shoot, and the yellow ones next to the pipes which you can use by activating them.