Floods should kill everything that can't breathe underwater. Flying creatures must land at some point. If there's no place to land, their dead. Creatures that can swim also die because eventually they get too tired to swim. So, we are left with creatures that can breathe underwater and those that don't breathe at all because everything will eventually sink below the surface of the water.
Nope, not all flying creatures must land. There are birds that can sleep while flying, and can feed without landing (eg. they catch fish or eat flying insects), they only land to breed.
Also, concerning flying creatures having to land, and swimming creatures getting tired... I guess a battle of elementals, though it lasts a few minutes from our perspective, it would probably last a few hours from 'their universe' perspective... I don't think it would last any longer than that, not days or weeks. A single turn probably lasts several minutes from their perspective, as in this time a creature can attack only once, an event like a rain of fire or an earthquake probably lasts also short (a rain of fire lasting half an hour would probably be much more devastating, so I guess it's more like a few minutes).
So a flood would be more like a tidal wave, a tsunami or something like that... an event that begins abruptly washing away anything that cannot swim or fly away, then lasts for some time drowning or washing away anything new that emerges on the battlefield... but it's still a short flood lasting a few hours (until the battle ends), so flying creatures would not get too tired in the meantime.
Also, why do you think a spark should survive the flood? (ok, you still have to buff it

)... I guess an electrical discharge in water would have a much harder time trying to keep it's form due to much better conductivity of ionized water than a typical air thingy...