If I continue to take my seizure medication, will my baby be affected?

Talk to your doctor. What medication are you taking? Some seizure medications are not recommended during pregnancy but it is also harmful to your baby if you have a seizure. You need to balance the risk and benefit, talk to your doctor about what is best for you.
Yes. Certain classes of seizure medications can be related to significant fetal abnormalities. Close communication with your ob/gyn and neurologist is very important.