As far as the historical nature of the water, all we know for a fact is they exist in the bodies of water today. Perhaps we can speculate they arrived at a later time than the Tannaim, etc. But whether that is the case or not, I don’t see how it effects the first two facts. “
They did not spontaneously generate. They were always here, but not readily visible to the naked eye. It is on that basis that many hold that the water is ok to drink. If it were assur to eat EVERY thing that had creatures swarming over it, but which we could not readily see, there would be NO food kosher to eat. There are living bacteria, germs, dust mites, etc.,etc., on virtually everything. If you would see what is sitting on your EYELIDS, it would make you throw up. But you can’t, because they are too tiny to be viewed without the help of a microscope. And thus it is with much of what we are finding in the water. They are seen with a microscope. If you can readily see them with the naked eye, then they are large enough for the water to require filtering.