The stock Denso signal relay has two circuits, one of which goes to the ECU to determine forward motion for the signal auto-cancel function. However there's no indication in your post that the ECU is damaged.
We recently had another member with a battery box full of water. He had removed the inner fender liner between the back tire and the battery box, and so his battery box may (or may not) have filled with water off the rear tire, I don't recall. See: http://rswarrior.com/forums/p/112132/919588.aspx
From your post I don't have other solutions except to dry everything out, be sure you have the top tray for the battery box that the ECU sits in, be sure you have the two rubber protectors that sit on each side rail under the seat, check every fuse, and then bit by bit visually search the wires in-and-from the battery box for an accessible wire that is A: not protected in a bundle and B: damaged or corroded (maybe even blue-green-ish).
If the problem was a relay or sensor you'd probably get an error code - but its a big topic so can't be sure.