I played against both an AI lvl 1, and an AI lvl3, and flooding doesn't kill ANY creatures.
Flooding has the following restrictions:
1. The creatures must be in a flooded area (not the first 5 spaces)
2. The death happens when the creature attacks (or fails to attack). If flooding is destroyed before then (because you couldn't afford the quanta drain, or because the AI destroyed it), they won't die.
3. The creatures must not be water element.
4. The creature must have an element (meaning malignant cells and shard of focus and a few flown weapons are immune).
5. The creatures must be target-able (not burrowed or immortal).
Testing in the trainer, I was able to kill enemy creatures with flooding. Please check that all the above conditions apply, and then post a screenshot of the creatures surviving when they should be dead (if applicable).