I couldn't pass this up, simply because the word "ship" is there, I think there must be a solution!
Personally, I can't get the image I once saw of a home in the middle of a flood
land where they decided to bring in tons of fill to essentially build a mound/moat that the dwelling sits on, surrounded by
water. I'd be sure to have a jon boat docked on the front porch :)
Other than that, crazy ideas like building the dwelling on a floating platform of sorts? that would rise with the water on large posts drilled and anchored into a rock layer below (sounds expensive and kind of ridiculous)...or simply up on posts to a level you think would keep you dry? But, kind of defeats the whole "earthship" idea in terms of being settled into the Earth for the benefits!
Is there an area of your property above water level? Then maybe you could think about a portable home that could be dragged or trailer'd to a higher temporary location, then brought back and hooked back into it's "Earthship" spot of some sorts, w/ relative ease.
If the old house is still there tho, and hasn't succumbed to the flooding after all those years, I'd imagine you could focus more on a permanent structure that could endure the conditions by improving the immediate land around it to keep the water away. Is there a basement? Even if you are on a mound, the mound could saturate
enough from the surrounding waters to flood an
underground area if its below the water line. How much water do you get?