I think there would be many times when crossing barefoot would be fine. However, a number of potential risks do exist.
Those can include:
- Getting scraped or cut on either the bottoms or sides of your feet. Culprits could be various sharp items, including broken shells, broken glass, pieces of fish hooks, bottle caps or other sharp litter.
- Stubbing your toes on rocks, pebbles, or unexpected items in the water.
- Slipping on rocks, or river bottom areas, that are wet or slimy from something like algae.
- Twisting an ankle or two due to lack of support.
- Being bitten by something in the water.
- Picking up a bacterial infection from something in the water
- Losing your balance as you go in or out of the water at the crossing point
In areas of very clear water, many obstacles can be avoided, and slipping would be the most likely problem. If the water is dark or murky, you're more likely to step on something just because you couldn't see it.
Some of the hazards might be more likely if you're carrying a backpack, especially if it's heavy. For instance, if the load shifts you may lose your footing more easily, whereas the support of a shoe might keep you more steady.
Also, if anyone in the group has a pre-existing condition that makes barefoot walking less than ideal to start with, they might be more susceptible to problems in the water. That's true for me. An old leg and foot injury left permanent problems (mostly lack of feeling in one foot) so I'm not even allowed to walk in the yard barefoot anymore. Your party has already decided to cross barefoot, so that's probably not an issue in this case!
My husband and I have crossed a lot of rocky streams in the White Mountains area of New Hampshire. We don't go barefoot, but love the feel of the water rushing on and around our feet. We wear flip-flop sandals with some texture under the foot and on the bottom of the sole. They give some support, and are lightweight and easy to carry. That doesn't technically answer your question, though. I just thought I'd share it as an alternative.