This is definitely a thing I think of as a GM tool. A flood is fundamentally a thing that overpowers a certain sort of character. If you don’t have magic that lets you get out of the way, a flood is a sort of plot that means your win condition is likely to be survival, not victory. It might be rescuing others or things you care about, but a flood’s ultimately about facing a huge thing that you can’t stop, and riding it or getting mashed but staying alive – or dying. It could be about dying.
In RuneQuest, the drowning rules are notoriously horrible. Wicked-bitching Nasty. I’ve got an alternative I use that’s a bit more realistic, and also a bit less arbitrary, but I can’t use that all the time because I play in a shared world with someone, and swapping rulesets is not a thing I want to get into.
So, how do I make a flood interesting for someone? I try to have safety nets, and to endanger things, not people. This can include making those who have magic use it, and then they’re out of magic. I also try to make floods an opt-in thing, or at least, something that can be avoided. Flash floods in wadis, the anger of water spirits, and slow-moving magic are more interesting than a dam giving way and a load of enforced rolls. There should be ways of getting out of the situation, or avoiding it1If you drift a raft through the wardings at Ogre Island, it’s your fault if you fall in the water. I don’t know what they were thinking. Probably that they were the heroes so it was all going to work out..
And then, because it’s RuneQuest, there should be a genuine risk of dying as well. This is one situation where the GM might point out your options, but she’s damn sure not going to take dying off the table as one of them.