Continuing the discussion on the “waters above the firmament,” St. Thomas writes,
“Some have attempted to solve this difficulty by supposing that in spite of the natural gravity of water, it is kept in its place above the firmament by the Divine power. Augustine, however will not admit this solution, but says ‘It is our business here to inquire how God has constituted the natures of His creatures, not how far it may have pleased Him to work on them by way of miracle.'”
Evidently he was clear on the distinction between the natural and the supernatural and, even in the 13th Century, didn’t feel the need to invoke miracles when the natural causes of something were unknown.