Floors ... ahh .. but with rotted floors usually comes rotted stringers, and transom is usually go hand in hand, most of all on Hydra-Sports .. I recently rebuilt a 87 Hydra .. started with floors ended up doing all the wood.
If it is JUST the floor, you have 2 options cut out just the rotted sections and replace those, or remove the top cap of the boat and replace them properly, but while the cap is off you may as well do all wood.
My Hydra had floor rot around rear drain, you can just cut back to good wood ( Cut edges in a v shape on the wood you cut out then , cut you replacement pieces at same angle on the new wood ) .. The hydra boats glue the top of the boat to the floor using a thickened polyester resin, you will have to break that with a chisel to be able remove rotted wood, and to slide new wood up under if the wood under the cap is rotted.
Your best bet is to use epoxy resin on the new floor sections, cover bottom side, the let cure, after cure is going good, slightly tacky install that wood in place , making a paste with the epoxy using milled fibers, and cab-o-sil to act as glue. set that in place then apply a heavy weight to the floor section and wait a good 24 -48 hrs before removing the weight.
Then grind any blobs or high spots with 36-48 grit until even with old floor, apply more epoxy to at least a 4 inch area around the patch, then using 1708 biaxal cloth wet that out make sure you get all the air bubbles out with a epoxy friendly roller. and wait another 3 days until fully cured.
You can get all the stuff you need to DIY at uscomposites.com
You can do the same process using polyester resin ( its cheaper per gallon 25 compared to 60-90 plus hardener ) but it wets out easier, and has very low odor, and is 100% water proof and bonds to wood much better than polyester, and polyester is not water proof.
You could use polyester resin then paint the entire floor with an epoxy paint but it would cost as much or more to do that way.
If your whole floor is bad, its much harder and would be best to remove the top cap to do whole floor. That way you can get it properly tied into the sides of the boat, gives it better structural strength .
Here is pics of my hydra restore
just follow the link it will show the whole project from day one including the floor
http://s29.photobucket.com/albums/c296/northrivergeek/Hydrasport restore/