It shouldn't be a problem, especially with the "magic" tag involved.
First, water isn't the greatest conductor of electricity. Even with a lot of salt in it, making it much better, it's still not that great.
Second, the electric charge will tend to go through the path of least resistance. If you have a high-charge positive and a floating ground connecting to the same system, and those electrodes are a couple millimeters apart, the path of least resistance will be from one electrode, directly to the other.
A little current may spread out and hit the user, especially since they're presumably wet and therefore grounded. But it should be minuscule. You can make a lot of the parts out of polymer, Glock-style, to mitigate the amount of current "escaping" the electrodes. (The electrons can't just run straight through the receiver, but instead have to run the long way around via less-conductive water.)
There's a video on YouTube of a guy putting 120V electrodes into a bucket of water, then sticking his fingers in the water. On his normal fingers, he was able to practically touch the electrodes before they shocked him. On his finger with an open cut, it was more noticeable, becoming painful half an inch away.
With salt added to the water, it didn't bother his normal finger until he again practically touched the electrode, although his cut finger he could only get a couple inches from the electrodes before it was painful. He was able to light an LED by sticking it in the water near the electrodes with salt, but not without.
Another YouTube video shows a guy activating a taser through distilled water with another guy's hand in the middle. Despite the hand being in the path of least resistance, there's no effect because the distilled water has so much resistance with just a couple inches of water to go through. After pouring a bunch of salt in (same video, advanced a couple minutes), there's a noticeable shock, but it doesn't send him into convulsions or anything.
If you're using a lot less than 50k volts, and/or doing it for only a tiny fraction of a second, I doubt it would have much effect.