The Marine Mammal Stranding Center says parasites and a possible respiratory infection could be to blame.
The rescue happened on February 7 after the pup hauled out from the bay at West Avenue between 42nd and 43rd streets.
He showed signs of improvement, but Monday night his health suddenly took a turn for the worse and he passed away.
A full necropsy will be performed to provide insight into what may have caused him to go down so quickly.
The stranding center said in a statement it wanted to "thank the residents of Ocean City and everyone who rallied around this little seal. We know that you are hurting as much as we are today."