Me and some of my outdoorsy friends argue about this.
I refuse to get in bodies of water that I cannot see the bottom of. Even if it is somewhere shallow like a creek.
I’m not saying that it is impossible to drown or to get injured/killed by other means in clear water, but I feel that because you can see what’s going on beneath you, clear water is inherently safer than murky water.
Some of my friends say that it doesn’t matter one way or the other.
What are you attempting to avoid? Holes and things that you could step in, or fish and other creatures that could “attack” you?
Apparently like SharkS., I’m finding it a bit hard to come up with examples of the lurking dangers that clear water allows the would-be swimmer to see and avoid.
If there was stuff you could get tangled up in maybe. Like if you jump off someone’s deck while at the cottage and there is a broken mooring line. Or you leap head first and bash your head on a rock you didn’t see.
But the OP says “even somewhere shallow like a creek”… Well, I guess wading over top broken bottles could cut your foot, but that same danger would exist in tall grass or deep snow.
I misread the title as “bottles of water” and couldn’t for the life of me figure out how there could be any question at all. 
In a creek, the danger I’d be most worried about would be stepping on a slippery rock and either falling or breaking an ankle.
Clear water allows you to employ an additional sense, and a mighty powerful one at that. In that regard I suppose you could say clear water should be at least as safe as murky water, all other considerations being equal.
The fact it’s clear doesn’t make it safer but it should allow you to judge the dangers with a greater degree of accuracy.
I think it’s fairly obvious that entering an environment in which you have sight is going to be safer, to some extent, than one where you can’t see anything. I suspect even your friends would agree with that. What they probably disagree with is that the difference in safety is significant enough to warrant your refusal to ever swim in murky water.
Personally I think it’s taking a big risk to get into any body of water which isn’t a common swimming area where lots of other people swim regularly, particularly if, as you say, the water is murky and you can’t see what’s under it.
My biggest concern is the inability to judge depth, spot currents, and snakes in murky waters.
As long as you aren’t in, say, Australia, the snakes are going to be on top of the water.
In Russia, snakes are sick of being in the bottom of YOU!
Being able to see is always going to be better than not, so I’d agree that clear water is safer. I can’t think of any predators that prefer clear water to murky.
The only case where this is not true is somewhere like Yellowstone where clear water tends to be either below 40 F or above 160 F.
However, I don’t think murky water presents much of a risk, whether we’re talking predatory animals, underwater hazards, etc. We might be talking the difference between 99.9% safe and 99.95% safe.
Snakes swim on the surface. Personally, I find cloudy water ever so slightly easier to judge current because crud in the water makes it easier to judge movement, but I don’t find much of a difference either way, to be honest, since most visual cues depend on surface disruption. Depth, sure, but sometimes it can be misleading (the ledge may not be as close as it appears…)
This may be more of an IMHO thread, come to think of it.
It’s the murkiness of the water that would disturb me, rather than fear of what might be on the bottom. I mean, the murk is from something, right? So if you go in the water, that something is going to be on you. No, thank you.