Drains are used in few levels in the game, but they are essential to the levels that they are featured in. They are always coupled with toxic water in levels.
The drains themselves do not make a physical appearance in the game, but they are indeed present outside of the level bounderies, sucking toxic water away and off the screen, opening new areas of the level to characters such as Thomas, Chris or Laura.
It is unclear where the toxic water ends up after being taken by these drains. It simply vanishes off screen as the drain pulls the water down towards it. The toxic water, while being pulled by a drain, looks similar to how it does when it falls from above as rain.