Usually, swan parents will not leave their cygnets alone until they are much older. Could the cygnet have been on the mother's back under her wings so you could not see it? Carrying the cygnets on the mother's back is normal behavior when the cygnet gets tired or cannot keep up.

If you had a strong storm and the cygnet got too wet, he may have taken a ride on mom's back. Yes, other causes such as disease or predation could have occurred. But, look to see if you see the family together. Sometimes, the mother will also keep the cygnets near the bank and hidden in the reeds from predators. Please let us know how this situation progresses. The Regal Swan