User blog comment:B214/Volume 21 info & spoilers/@comment-197.113.0.82-20160422102238/@comment-24.113.129.70-20160423041152

From what was said in the light novel, "Primordial Water" is basically Apophis creating a giant orb that blocks out the sun (makes an artificial solar eclipse) and black water leaks out from that orb. I don't know for sure, but I theorize that the black water not only drowns you, but also reduces you to nothingness,  similar to the "Dimensional Gap."

Another way I could say this is that it might be a water version of the Bael clan's "Power of Destruction." It drowns and destroys.