First off, mucking about in waters gr8 but if you want to keep your wagon for the long term you'll have to put the work in maintenance wise, the slightest but of water in your lump + its an engine swap. I say this as some defender models are quirky -the Td5 for example has a tendency to shear the pegs of the intake manifold -extra things like this need to be considered or its a watery grave!
For all models i would say yes check the drain 'fanny' -there's one in your heater intake too- but be more concerned about sealing vital stuff -a Gucci snorkel's as much use as tits on fish if your air filter seal or any of the ducting's on its way out -same for the turbo ducting (i just found a tiny hole in mine from chafing against a hydraulic line -luckily the recent floodwater round here wasn't high enough to reach it)
if your playing in water that's likely to get into your battery box + fill up to your battery's breather then fit a sealed battery instead -certain types of battery tend to explode if water gets in!
a good quality sealed gel one is a good investment anyway. iv sealed my battery box with mastik too.
if your serious about wading then move the fuse box (or mod' into a sealed container) -it might not fail anything the first or second time you fill it with water but the minerals (even in fresh water) will build up on the contacts + eats /bridges the copper connections when left for a while.
Dow corning make an excellent electrical connector compound that i would suggest you fill every connector you can get to to keep out water.
For a wade day, there's also a white sealing putty (i got some on ebay -said it was for caravans but its the same as the Mod stuff) put this round anything you don't want water getting into -iv put this round my snorkel where it meets the bulkhead as extra protection+ i also seal the battery compartment lid with this + peel it off after.
check your axle breathers regularly - as im sure you know, the cold water hitting a redders diff causes a vacuum which -if the breathers are even slightly crudded up- can fail the gaskets.
also, if your in snorkel territory then afterward, rinse down thoroughly from hosepipe water -iv seen 2 civvi wagons spontaneously start smoking after a wade where waters penetrated the loom. (again mineral action from fresh water + salt waters even worse so watch those tidal fords!)
If the water that you'll regularly ford is particularly silty, keep an eye on your handbrake drum -these tend to trap the silt + are a nightmare when you eventually need to change the shoes!
wading blankets -worth their weight in gold!
Ref alternator -at work when we wade from landing craft onto a beach there's 6+hours of prep to make the wagon stage B waterproof, this includes disconnecting the alternators to just run off the battery -i know its not great long term practice for a privately owned wagon but something to think about.
After that its down to your maintenance, rinse, clean, re grease EVERYTHING + check!
(Esp check / grease your engine bay, gear + transfer box earthing points -after a few fords these will start to corrode then you start to get random electrical issues!)
Enjoy!