Natalia’s navy
Well, it's clear that the rabbits under Whitson Mariner got into shipbuilding, if it hadn't been an art they practiced previously. Obviously they used ships to travel to Natalia, then on Ayman Lake, and later as they made their way from Ayman Lake to the Great Wood. Judging by Helmer, Hewson, and Picket's conversation in *Ember Rising*, the navy by the time of Helmer and Hewson's youth was a virtually unchallenged force dominating Natalia's waters. From the map of Natalia as we have it, these may have included:
Ayman Lake itself
The Rivers Flint and Fay, except those stretches that were under Preylord control
Lake Merle
The Goforth River, which flowed out of Lake Merle
Black Lake
Red Lake
The River Gale, branches of which flow into both the aforementioned lakes as well as smaller bodies of water near Vandalia and Harbone
Now, after the fall of King Jupiter, the navy has, so far as we know, vanished. Certainly there are no water engagements in the main series, at least not until *Ember's End*. Helmer even refers to the sailors of Natalia in the past tense, seemingly indicating that they're no longer a presence. The question is, what happened to them?
It seems likely that, like the army, Natalia's navy fell victim to the machinations of Garten Longtreader and his Preylord allies. Perhaps, having long gone unchallenged by any adversary, it was particularly easy for the sailors to be lured into a trap or taken unawares. Presumably, this ambush saw the navy personnel of rabbitkind either killed or captured and enslaved. As for their ships, these were probably either destroyed or, I like to think, seized by the predators for their own use.
Under this supposition, the wolf fleet that sails into First Warren in *Ember's End* is, in fact, the old rabbit fleet seized after the fall of King Jupiter. It has been maintained, no doubt, by rabbits either enslaved during or after its seizure or who else willingly collaborated with the new regime. Admittedly, the wolves may have been capable of building their own ships, but that seems a tad out of character for them. Even if they could, I feel like any captured rabbit vessels would probably be of higher quality.
Meanwhile, most of the captured sailors, shipwrights, and assorted other naval personnel would likely have been carried off to Akolan. It would have amused the Preylords, no doubt, to secure the rabbits who once dominated the water so far from any of the rivers or lakes they once sailed without fear. But in doing this, they actually help set the stage for their own eventual downfall. Because as it happens, there is a scheme for the rabbit slaves to escape Akolan by water. A scheme that needs few things more than rabbits trained not only in combat, but in the construction and operation of ships and the kinds of weapons you fight with aboard them.
It's almost like the story of the Portuguese Navy. A once powerful navy in the 15th to around the 17th century and its downfall.