Did you ever find out how to fix this? I am having the same issue

Geraniums hate wet feet and that's your problem. unless the stem at the bottom has blackened they should be all right once they dry out. If the stem is black that's black leg, a fungal disease the plants a goner. There is no cure.

If there's a way to move them to a dryer location or cover them and the soil if there's more rain I'd do it