Rain is usually white and falls like normal rain would. It is assumed that it is made from the same elements as toxic water, yet it does not affect Thomas and the others, with the exception being Claire, who is immune to toxic water anyway.
The rain itself does not pose any threat, but it can contribute to the threat of toxic water. Falling from above, it can add to an existing pool of toxic water and cause it to rise higher and higher, forcing the characters to reach their portals faster.
Some rain takes the form of simple water that fall when a character presses a button. This often causes an existing pool of toxic water to rise.