So with all these partly rainy days, for lakes that are large and clean (for Texas) like Canyon and Medina, will a bit of rain for several day in a row really mess up the visibility that much? I am trying to figure out where the heck to go fishing this weekend and it looks like the whole southern half of Texas is affected, though further south will have a few less days of rain than south central.

Most likely the upper ends of the lakes will muddy up some, but the main bodies and lower ends should stay relatively clear. The lower ends will only muddy up if they open the gates and really start letting out a lot of water. Size also matters. The larger lakes tend to stay clear longer than the smaller lakes.

For the lakes that you mentioned, if you find a spot where a natural spring starts to flow due to recent rain, I have found more fish in the immediate area.

Minimal impact on both lakes from my experience.