To complete the Trial of Matter, April persuades Crow to bring her a beakful of this water in order to create a bridge to the Tower, in spite of his fear of putting such powerful magic in his mouth. When she crosses the bridge to the Well itself, April places the Stone Disk in the Well to open the way to the Tower. This causes a handprint made from water to form, which responds to the touch of a true Guardian (though not to April, much to her surprise).
In Dreamfall, since the collapse of the Tower, the Well of Making appears to have been sealed, with the Guardian suspended above it instead of within the Tower itself. A spiral of blue light is visible beneath the Guardian's feet; the channel of light he is caught in appears to be generated from around the Well's seal.