Why Does My Pee Smell Bad? Often, pee with a strong odor simply means that at the time it is very concentrated; there just isn’t enough water in the body to let the urine be at its normal consistency. Thus the urea, highly concentrated in the urine, smells, often times strongly of ammonia. Any sort of dehydration can cause this, even because of being in bed for a few hours, which is why urine can smell in the morning, just after you’ve woken up.