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.
outdoors.stackexchange.com/users/5547/Sue Saddest Farewell TGO GL
The principal risk is that you will slip and fall.
Depending on the force of the water and what is downstream, this could be serious.
Look at the tread on your hiking boot or running shoe or even tennis shoe, and then look at the sole of your foot.
Unless you can pick out a sandy route with no rocks to cross the stream, it is pretty obvious that there will be more friction between the streambed and the shoe than between the streambed and your bare foot, i.e., you will be less likely to slip and fall.
The better grip of your shoes also allows you to cross the stream faster.
A secondary benefit of crossing with your shoes on is that very cold mountain streams will feel much less cold if your feet are insulated by boots and socks.
Yes, your shoes will get wet.
But you can pour the water out and pat much of the moisture out with a towel or sweatshirt.
You can also change to dry socks.
If you have more streams to cross than you have pairs of dry socks, wear a thin undersock of some very low friction material to protect your feet against chafing.
outdoors.stackexchange.com/users/6411/ab2
Barefoot danger possibilities:
Nails, broken glass, discarded can lids, sharp rocks, ripping off toenails, general cuts and scrapes, lots more.
After trying various options, including barefoot, I'm going to buy light sandals for around camp, hiking on wet days, and stream crossings.
I can't hike in wet shoes, even if I cross with shoes but sockless and put my dry socks back on after letting my feet also dry.
Just no good for me.
If you want to experiment carefully, sacrifice a pair of thick socks (i.e., get them wet).
Stockingfoot waders (which I've never personally used) have felt soles.
Fuzzy dense fabric like that grips wet rocks far better than any rubber and will offer some protection, including (maybe) slipping off if you get a foot trapped between or under rocks.
outdoors.stackexchange.com/users/12993/davesailer
Helminthiasis of various kinds does not even rely on open wounds.
Schistosomiasis is particularly ugly and is on the incline.
You did not specify just where you are backpacking: there may be other parasites around.
Of course, with organized backpacking trails, a certain ratio of the group is expected to use new shoes etc and thus is likely to get blisters or other kinds of potentially open sores at the feet that are great for bacterial infections.
This goes in two directions:
feet softened by exposure to water are more likely to break open when continuing the hike.
Some blisters are a matter of timing: the risk of infection is lower when the blister has had enough time to run its natural course before breaking.
And slipping in a river bed is a real danger and can easily lead to twisted ankles for people used to the support of hiking boots.
So all in all I consider it likely that the statistics for forcing people to wear solid footwear when crossing are favorable for keeping incidents down.
outdoors.stackexchange.com/users/13003/user13003
We do it often in the Philippines.
But you can cut your feet.
We find there a pair of flip flops improve traction.
Easy to pack.
Rocks can be slick.
outdoors.stackexchange.com/users/12302/J Bergen
Sometimes while backpacking you have to cross streams, and from a weight point of view, it would be nicer to just cross in your bare feet, instead of bringing an extra pair of shoes along.   These situations wouldn't be raging rivers but rather streams that can't be crossed without getting your feet wet, where crossing in bare feet seems like the simple solution.  However, I have seen outdoor backpacking organizations mandate closed-toed shoes for all stream crossings.  What are the risks of crossing a stream with bare feet?
What are the risks of stream crossing with bare feet?
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<safety><backpacking><rivers>
outdoors.stackexchange.com/questions/15973
outdoors.stackexchange.com/users/8794/Charlie Brumbaugh
Crossing barefoot would often be fine. However, risks include getting scraped or cut on either the bottoms or sides of your feet on sharp items, slipping on rocks and twisting ankles. You may be bitten by something in the water and diseases can occur, including helminthiasis and schistosomiasis. Bacterial infections, being bitten, cuts, slips, falls and twisting your ankle are risks.
Being bitten or getting a bacterial infection are risks. You may cut your feet. You could slip on rocks and twist an ankle or fall.