Simple explanation is to locate where your Aeroscenery Ortho Images are saved, click on 'stitched' folder, edit your ortho photos (I use GIMP for free) by either cropping and deleting that part of water or by blending in the proper color to match the water. This is why locations along waters can be a pain in the booty.
Edit: Just noticed you used FSET. Same concept though for editing.