Normally, the vagina produces secretions which keep it moist and these increase when you become sexually aroused.
These may include fibroids that can cause deep intercourse pain. When this occurs, the pain can be resolved if the female becomes more relaxed, if the amount of foreplay is increased, or if the couple uses a sexual lubricant.
Female Pain & Sex
Female Pain During Sexual Intercourse: Causes & Treatments
Dyspareunia (Pain Having Sex). Medical Information
Certain medications are known to affect sexual desire or arousal, which can decrease lubrication and make sex painful.
Such problems might include cysts on the ovaries. This is common during passionate sexual relations, and can come and go depending on the position used during intercourse.