Nighttime heartburn may be particularly dangerous. Waking up with a sour taste in the mouth, coughing, or sore throat may indicate nighttime acid reflux. Not only does it disturb sleep, but the esophagus may sustain more damage. That’s because when you are lying down for several hours, acid has a lot of time to linger in the esophagus and damage the tissue. When we are awake, we swallow saliva throughout the day. Saliva helps neutralize stomach acid. We naturally swallow less saliva when we sleep, so stomach acid is not neutralized.