Hydrophones are the thing for recording sounds in water; but in shallow water, rigging them can be tricky. Here's my idea for this.
This video is pretty much obsolete now, as it's covered much better in the "Sound in Contact" episode. But I'll leave it here for now. (This was the first field recording video I made, as a trial run.)
Your hydrophones may be heavier than water, or lighter, or about neutral. In any case, using them in shallow water may be tricky; you don't want them floating away, but you also don't want them scraping on the bottom. And you definitely don't want them getting caught between rocks when you pull them back in, so that the cables get ripped out of the mics.
Here's how I rig my hydrophones to float free of the bottom without drifting, and also make it possible to recover them more safely. This technique works well in still or slow-moving water; it's not so great in fast streams, where it tends to get pushed flat. Of course there's going to be some risk any time you put expensive mics out into water, particularly with rocks, but this rig helps a lot.
