When one thinks of the Deluge, questions arise, such as "where did the water come from to make the flood; and where did it go to after the many months it is said to have covered the earth?" To the first the simplest answer is "from the place whence the earth and its oceans came:"—the whole being greater than its part, it may be inferred that the source which supplied the whole could easily supply an inferior part:—and, to the second question,—"part turned into earth, by combination with metallic bases; part absorbed by, and now held in the earth; and part evaporated." We know nothing of the state of the earth, or atmosphere surrounding it, before the Flood; therefore it is idle and unphilosophical to reason on it, without a fact to rely on. We do not know whether it moved in the same orbit; or turned on its axis in a precisely similar manner;—whether it had then huge masses of ice near the poles;—or whether the moon was nearer to it, or farther off. Believers in the Bible know, however, that the life of man was very much longer than it now is, a singular fact, which seems to indicate some difference in atmosphere, or food, or in some other physical influence. It is not so probable that the constitution of man was very different (because we see that human peculiarities are transmitted from father to son), as it is to suppose that there was a difference in the region where he existed.
This was for public consumption, however, as he privately told a friend at the time that he didn’t see how a “forty days flood” could possibly have caused the geological processes he’d seen. He would have a change of heart in later life.
After a few years serving as governor of New Zealand, Fitzroy returned to England and eventually founded what was to become the modern Meteorological Office. He invented several types of barometers and was the first to systematically collect weather data and to publish charts to aid in weather prediction. Fitzroy invented the term “weather forecast” and his 1863 Weather Book was decades ahead of its time.
The publication of On The Origin Of Species led to a final crisis of spirit for Fitzroy. He denounced the implications of Darwin’s theory, going so far as to show up at an 1863 meeting of the British Association for the Advancement of Science brandishing a bible and shouting at the audience to “believe in God rather than man.”
Fitzroy had been suffering depression and committed suicide in his washroom later that year.
Two excellent biographies of Fitzroy exist, each concentrating on different aspects of his life: Evolution's Captain: The Story of the Kidnapping That Led To Charles Darwin's Voyage Aboard The Beagle by Peter Nichols and Fitzroy: The Remarkable Story of Darwin's Captain And The Invention of The Weather Forecast by John and Mary Gribbin.
Fitzroy's own Narrative of the surveying voyages of His Majesty's Ships Adventure and Beagle between the years 1826 and 1836, describing their examination of the southern shores of South America, and the Beagle's circumnavigation of the globe can be found at Google Books here.
Darwin's Voyage of the Beagle, also at Google Books here, is his account of the trip and the foundation for later works On The Origin Of Species and The Descent Of Man.