Are you (I already know I'm super far off with this, but what the heck)
In the beginning I was as running Water
At the beginning of the water cycle, the water runs along the ground.
Then I was only running - fast!
When it evaporates, it's almost like running up into the sky to form clouds.
(but the Water stayed - in my Title)
The water becomes "water vapour", so the word water stays in the title even though it's not liquid water.
Don't you want to go to school?
Rain/acid rain/snow can sometimes cause school closures if it's truly, truly bad enough.
Here, try and awake me in my glass Tower!
A tower in the sky, ie. a raincloud? Or maybe this refers to the smokestacks which give off atmospheric pollutants which cause acid rain.
Beware of my Cycle: unlike my simile,
Acid rain becoming part of the water cycle is something to beware of.
My clouds will not bring Life.
Don't stand in the acid rain, that's for sure.