I've always assumed that when Thales said that everything comes from water, he meant this symbolically, not literally. Water or the ocean in dreams or mythology is a common symbol for what we now call the psyche, or in Jung's terms the collective unconscious.

A comparison can be made with Genesis chapter 1 where God creates the waters, then separates them into two levels. He then says: “Let the waters under the sky be gathered together into one place, and let the dry land appear”. This can be interpreted as meaning that the material level emerges from a more fluid, 'watery' level. In similar vein Thales has been quoted as saying: “the earth is supported by water on which it rides like a ship”. From this we can assume that he does not believe that the earth is literally made of water. He is clearly saying that earth and water are different levels.

This also seems to be the conclusion of modern quantum physics, that the material level emerges from a more fluid, i.e. less solid, quantum level. For example:

“Quantum gravity models predict that space-time is a seething foam of tiny regions where miniscule new dimensions unfurl and then furl back in on themselves, spontaneously appearing and disappearing with inconceivable quickness. These regions blink in and out of existence like the bubbles in the foam of a freshly poured beer. There is no such thing as empty space; there is only ‘quantum foam,’ everywhere. Such is space-time for a quantum physicist”. [https://phys.org/news/2016-01-quantum-foam.html]