Waters in waiting
The word translated "gathered together" is the verb קָוָה (qavah). Though from a root meaning "to bind together", this word is most often used to convey the idea of waiting patiently, especially on the LORD. Since God commands that the waters upon the earth be gathered, it must be for a purpose.
The waters had run free in chaos. But they were suddenly contained with limits. The mechanism is a mystery, but the origen of the verb may provide a clue. The gathering together is associated with twisting, as in making rope.
Water is drawn into a vortex when provide an exit from it's settled state. This is seen in drains and waterspouts. It is consistent with the text and science to suppose that the subterranean cavities were opened to provide the underground irrigation needed on the young earth.