My understanding/interpretation:
For running water to shut down magic, it has to be established as a threshold first. It has much to do with large bodies of water being actual physical barriers as well. Water is not shorting out magic everywhere, it does so when it is also a (somewhat) physical barrier. A river, a stream running down the street, a lake, those sort of things. Canalization for example can hold more running water than a small stream, but if it would actually affect magic, an urban wizard would be almost impossible. It is underground and it does not affect anyone in any way, so it does not short out magic.
Back to water magic:
Since the water the wizard is moving is not going to be a threshold, it does not influence magic other than maybe extinguishing fire. Moving enough water to actually have it be a threshold is probably impossible using evocation. Even a small stream will run for a long time and hold a lot more water than a quick burst of water ever could.
Let's paint a picture:
If you are covered in mud, you will still be mostly covered in mud after someone tosses a bucket of water over you. You'd need a good long shower to get all that mud off.
I imagine the same being true for magic. Just getting wet is not going to cause you to short out your magic. Even light to medium rain won't do the trick.
A good mundane countermeasure against supernaturals actually is a fire truck. Those things can pump 300+ liters per minute, and provided they have enough water to draw from, they can keep it up for quite some time. Keeping up a stream of water like that is not going to be quite hard for a wizard to do.
However, a wizard could pierce a water tank to create a stream of water that can then be established as a threshold. or ripping down water pipes can work, too, if they are not shut down by some security measures.
The fire truck actually gives me a great idea for a mundane monster hunting group.