By the Flood, I'm assuming the one where Noah had to build an ark on God's orders with two of every animal boarding it.
The major differences between these two concepts is that the glacier theories explain how the Flood occurred on Earth naturally, due to Earth's many catastrophic events. The Bible, however, pinpoints God as the primary reason for the Flood by supernatural means. The glacier theories are more factual and have evidence behind it while the Bible is not scientifically proven.