Rabbits are prone to a few nasty infections that can start with an innocent looking runny eye, and develop into something much more sinister. Pasteurella, Bordetella, and Staphylococcus are all commonly implicated when rabbits start developing discharge from their eyes, and if allowed to persist, can quickly spread into the respiratory tract. If flushing doesn't fix the problem in a day or two, or if you notice a whitish color to the discharge, any associated sniffling/sneezing, or if the rabbit's behavior seems at all "off" I would see her to a vet to make sure something nasty isn't brewing.
Also: what is she bedded on right now? Some beddings can cause eye irritation, particularly those that are dusty, as can ammonia if you get behind on cleaning. If there's been no recent change in bedding or cleaning regimen and you've had the rabbit a while it's *probably* not the cause, but it's always something to consider. One of my does had runny eyes once because we used to bed on hay and got an exceptionally dusty bale, so if you're bedding on anything that can vary from bale to bale (or package to package) also be mindful of that.