It's quite normal for almost people to feel eyes watery when they make up themselves with eyeliner. It is a commen phenomenon to get eyes water when your nerve system is stimulated. The most possible reason is your skin, especially your eyes are not suitable for brands of eyeliner that you are applying, which will stimulate the eye nerves. Thus, your eyes will automatically produce some tears to keep them moist, which is the reason why your eyes always watery when you use eyeliner. It is not a serious problem, if you really feel uncomfortable, just take some eye drops, next close your eyes to stay fit, maybe you will see changes. However, if these solutions do not work or the symptom become worse, you'd better see a doctor to get a physical examination.