My players have really latched onto the idea that running water disrupts magic in the DFRPG setting. One of them is asking to have a water-gun in order to mess up another caster's magic. Another used his need to go to the bathroom in a fairly interesting way. My question is how limited is the use of running water? How much water should be needed in order to disrupt the effect of someone's spell? The exact circumstances in one case were that one of them tried urinating on another's earth wall to undo it.
There are two sides to this coin. One is how it should be handled if you're hewing close to the source material, and the other is that you don't have to be beholden to the Dresdenverse canon in the first place if you have better ideas.
I'll start with how it "should" be done, if we're assuming a more-or-less faithful adherence to the Dresdenverse and DFRPG's representation of it. That'll give us a baseline for the second part, too.
Canon Dresdenverse: A trickle is not enough
Flowing water mystical "grounds" magic, but only if there is a significant flow of it that goes from somewhere to somewhere ("Thresholds", YS230). The analogy is to an electrical Earth ground, with rivers and lots of water pipes acting on magic exactly like a lightning rod acts on lightning: it draws it away from wherever it would have gone and harmlessly dissipates it. Flowing water also only grounds out magic that tries to cross over or through it.
A trickle of water (or mostly-water) isn't grounded, and is rarely going to be manueverable into position so that the magic the PC wants to target can be considered trying to "cross" it. Widdling on a magically-sustained earthen wall isn't creating a Threshold that will sap the magic from it! Similarly, a watergun won't create a meaningful threshold. Trying to use portable water to disrupt a spell being cast is unlikely to have any effect at all... but if it did have an effect, it would be like sticking a copper wire into a live power outlet and hoping to "disarm" the electricity—obviously a misguided strategy!
To have any effect on magic as a threshold, a flow of water has to be significant and the magic has to try to cross it. That limits it to rivers, water mains pumping stations, a full-blast fire hose (both itself and its output), battles in the storm sewers, streets flooded by torrential downpours (but not the rain itself), and similar significant flows. Note that all of those will have different strengths of threshold! The Potomac is going to have a much higher threshold than a fire hose, even if they both count as "significant", and setting those exact numbers is your job. Proximity, "openness", and the kind of movement involved matter too for what counts as "crossing"—a water main flowing twelve feet under 28th Street doesn't seem to matter to a Black Court vampire, but opening a main valve to create a flow of water can get in their way (first example on YS116), and casting a tracking spell with water pipes surrounding you creates a threshold the magic has to cross to reach its target (second example on the same page). So the Potomac might have a very high threshold, but it won't stop a tracking spell unless the target (or caster!) is at the bottom of the river.
The result of this treatment of flowing water creates a dynamic that is recognisable from real-world mythology and legends.
But it's not the only way, if you want your world to work differently.
It's your world: go nuts
DFRPG is very explicit about giving the GM the power to rewrite and override Dresdenverse canon: after all, the novels and the RPG are only what fallible people have reported to be true in case files and a game written by a werewolf, and come with no guarantees of accuracy or completeness. There's lots out there that Harry hasn't run into yet, and Harry has been known to be wrong on several occasions. Your Story is going to be different in small or large ways, as you prefer.
So you could totally make small amounts of flowing water disrupt magic just by its presence. To guide you in adjudicating this during play, you should come up with some kind of metaphysical rules of thumb for how and why this is, so that you can quickly determine what will and won't work and what it can do. For example, you could decide that moving water "jams" the flow of magical energies; as a consequence, the watergun idea might work if the PC manages to target the contact in the way of the forming spell or the magic's outgoing direction, but the creative urination trick maybe doesn't because the flow isn't "getting in the way" of anything and so doesn't jam the magic. Alternatively you could decide that any amount of water acts like a "sink" for magic and sucks it away (to where?), which would make both strategies work, maybe modelled as attacks (for the urination) or blocks (for the watergun). Again, those are only examples—whatever you might come up with is almost certainly going to fit your desired world better than something Random Q. Internetter comes up with as an example.
The other thing to consider is the larger consequences—the PCs wouldn't be the only ones to discover this, these effects of small amounts of water would have been well-known for centuries. How does that change your world compared to the "canon" Dresdenverse? Water becomes a powerful anti-magic tool, and its use will be pretty wide-spread. You might end up logically concluding that the Monsters on the other side of the Unseelie Accords now carry water balloons—effectively anti-magic analogues of small EMP grenades—as a standard piece of kit.
However you decide it works, be consistent and spend a bit of time (maybe not all at once—you can explore the implications of water's mystical effects piecemeal along with your players, as the campaign progresses) figuring out how magic and water interact, and the consequences on people and politics that has.