If a creature would deal combat damage to Ironscale Hydra, prevent that damage and put a +1/+1 counter on Ironscale Hydra.
If damage that can’t be prevented is dealt to Ironscale Hydra, the damage is dealt and you’ll simultaneously put a +1/+1 counter on it, before the game checks for lethal damage.
You put only one +1/+1 counter on Ironscale Hydra per creature whose combat damage is prevented, no matter how much damage would have been dealt.