First of all, the flood in The Epic of Gilgamesh lasted seven days. Noah's flood lasted one year and 10 days. This is one major reason why the two floods are different. Uh... I don't know what else to say about this...
Secondly, the flood in the story is caused by a bunch of gods, not a single God. This fact is very important in understanding the difference between the two floods. In the Bible, God tells Noah about the flood. In The Epic of Gilgamesh, the god Ea tells Utnapishtim about it.
Finally, in The Epic