In scripture, when God performs a miracle it is clearly identified as a miracle. It has a specific time and place, context and purpose. It is to demonstrate God's power and sovereignty over the natural world when such a demonstration serves His own end.
The original Creation must be called a miracle, of course, but what God created was a universe ordered by laws. Nevertheless a believer knows that God is working at every moment to bring about His purposes, including through the operation of those laws. A miracle would be His suspending the normal operation of those laws to demonstrate that He is God who can do so. But He also works through them at all times.
When it comes to the Flood, there is no hint in the Bible that anything miraculous took place. God said a great flood was coming, Noah preached it and built an ark out of faith that God was telling the truth. It took him over a hundred years to build. These are pretty mundane facts. When the rains began, this was a new thing on earth, but there is no hint it was anything other than the working out of conditions and laws already in place.
Science itself depends upon a lawful orderly universe, the kind of universe God made. There is absolutely nothing that exists that does not depend upon God and that certainly includes science. But surely it is obvious that we say evolution denies God because it denies what He tells us in His written revelation about the creation of humanity and about the flood. Nothing mysterious about this.
Edited by Faith, : No reason given.
Edited by Faith, : changed "operates" to "works" in a couple of places
™ Version 4.2
