You don't even need watercooling for really good thermal control on a desktop. Companies like Noctua make CPU fans that are just as effective, quieter, and are less complex than watercoolers (and I say this having built a watercooled system in the past year).
Watercoolers do have fans, so not only can you run into potential "fan issues" but you can also have a "pump issue" on top of that.