Horses will be highly reluctant to enter water which has overhanging branches or if they can't see the bottom. I've had more than one argument with a horse that was terrified to cross a stream because the water was "up" a little and muddy.
The reasons are pretty simple.
Overhanging branches can conceal ambush predators.
If you can't see the bottom it might be muddy, sticky, slippery or otherwise unsafe.
This is why water obstacles are included on cross country courses. They are a test of how much the horse trusts their rider and how willing they are to go into strange water on the human's assurance that it's safe.