Perhaps a powerful and corrupted spirit that guards Merlin's Castle and sees Harry and his friends as intruders. This spirit might have its own evil agenda and try to stop Harry from achieving whatever goal he has in the castle, like obtaining a powerful artifact or knowledge. It could use all sorts of dark magic and illusions to deceive and harm them.
One possible plot could be that Harry discovers a hidden passage in Hogwarts that leads to Merlin's Castle. There, he finds ancient spells and artifacts that help him in his fight against Voldemort. Maybe he even meets a ghostly form of Merlin who gives him advice.
Morgana could be a great antagonist. She might see Merlin's sister as a threat to her own plans for Camelot. Maybe she discovers that Merlin's sister has a power that could undermine her magic or her influence over the court.
It could be a rogue Death Eater who survived Voldemort's fall and blames Harry and his sister for the downfall of their cause. This Death Eater might be more cunning and powerful than the others, and he targets Harry's sister specifically because she represents a new threat to their dark plans. He might try to use her as a pawn to draw Harry out and then destroy them both.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
Well, it could be Agravaine. He's always looking for ways to gain power and influence in Camelot. If he finds out about Merlin as a borrower and the unique situation, he might try to use it to his advantage. He could either try to expose Merlin to gain favor with Uther or try to control Merlin and use his magic for his own dark purposes. Also, there could be a group of anti - borrower humans in the castle. They might be superstitious or just plain cruel and they could be the main antagonists as they try to hunt down Merlin and the other borrowers.
Maybe there could be a new antagonist, a dark shapeshifter who is jealous of Harry's power. This antagonist could be an old wizard who has been in hiding for centuries, waiting for the right time to emerge and take over the wizarding world. He sees Harry as a threat to his plans and tries to eliminate him.
Another possibility is a corrupted member of the Ministry of Magic. They might be trying to use Harry as a scapegoat to gain more power within the Ministry. They could be working with the Death Eaters or acting on their own, but they would be a significant obstacle for Harry as he tries to stay alive and free while on the run.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.
It could be Voldemort. He might see Harry's new waterbending ability as a threat and try to find a way to counter it. Maybe he would seek out dark magic related to fire to oppose Harry's water powers.
It could be a new dark wizard who has risen to power. This wizard might see Harry as a threat to his plans, so he manipulates the situation to get Harry exiled.