Jamieson, Fausset and Brown on 2 Peter 3:6

6. Whereby--Greek, "By which" (plural). By means of which heavens and earth (in respect to the WATERS which flowed together from both) the then world perished (that is, in respect to its occupants, men and animals, and its then existing order: not was annihilated); for in the flood "the fountains of the great deep were broken up" from the earth (1) below, and "the windows of heaven" (2) above "were opened." The earth was deluged by that water out of which it had originally risen.