What are these?

[Still Kicking]

That's the key. People have used rocks of around this size for ballast for time immemorial. But why go to the time and expense of bagging them?

I'm going with the rocks were ballast in some type of underwater drugs delivery or handoff that took place on that spot. The bags would be to keep dirt out of the payload or make sure some of it didn't cling to the rocks.

Or maybe to weight illegal fishing nets? But again why bag them?

As a one-time police reporter and watcher of hundreds of police procedurals (with varying degrees of authenticity), i can pretty safely say that drugs are never tranported loose. Even more so anywhere near water.

My guess is they have something to do with fishing. It is hard to tie a rock to a net but you can tie a bag to a net. Not sure why they dump the rocks afterwards ... maybe it's illegal fishing and it's easier to hide a net without weights?

Good job on the cleanup regardless.