It’s down to what’s known as the ‘nasal cycle’. We might not realise it, but our bodies deliberately direct the airflow more through one nostril than the other, switching between nostrils every few hours. A constant airflow can dry out the nostrils, which damages their lining, so giving one nostril a rest helps prevent this from happening.
When we have a cold, the blood vessels in the nose dilate as part of the body’s immune response, and the nose also produces more mucus. Both of these changes cause congestion, but you’ll feel more blocked in the nostril that’s currently ‘off duty’. The nostril with the full airflow might feel fine.