I am thinking of a few ideas for using water effect on some of the figures, but not sure how to go about it. I've used water effects before, but with Warmachine models. Their bases are recessed so the "water" stays in place. Has anyone done anything similar with Runewars Miniatures?

its a nice idea. i think you could ue a tape around the base to keep the paint in place

I've seen this done with a two part clear resin (one that sets in reasonably fast to give it less time to leak out) and good packing tape wrapped tight around the base.

That's standing water like this:

(This I believe you'll find easily on Youtube under "Water bases")

For puddles I'd put a bit of greenstuff on the base, put a ditch here and there, texture it, paint it and then fill it with the water effects stuff.

I didn't use epoxy/resin, but I do use vallejo water effects (still mostly, sometimes the gel for ripples and such) Funny you ask today as I just finished one up.

So I took a tray, and I cut out foam to fit into the tray, and cut out the cavalry plate.
Then I built up the banks a bit, shallow here really, as I didn't want too deep a tray, with earth effect stuff.
Painting the base entirely
added water effect to desired thickness, had a temporary cavalry in the tray with a tape dam (tape dam on outside as well) beware Vallejo still water has pretty huge surface tension, it will curve at edges. I trimmed this later. I colour the water affect as well.
Applied some ripples mostly one sided and on shores to give the stream flow and direction.