Something flooded is overflowing with water. A flooded river bursts over its banks, covering the surrounding land.
If your basement is flooded, it's full of water, and anything you keep down there is floating around in it. Entire towns can be flooded as well, particularly coastal cities during torrential storms like hurricanes. You can also describe someone's eyes brimming with tears as flooded. The word comes from flood, which has an Old English root, flōd, "tide, deluge, sea, or wave."