One possible reason could be the stress of his ninja duties. He has so many missions and responsibilities that his mind is constantly racing, making it hard to relax and fall asleep.
Maybe he had a bad experience as a kid. Like he almost drowned once, and that made him too scared to learn how to swim properly.
One possible reason could be that he was severely injured in a battle. Maybe he got his legs broken or had some internal damage that affected his ability to move them. For example, if he fought against a really powerful enemy who used a jutsu specifically targeting his legs, it could leave him unable to walk.
One possible reason could be a powerful jutsu gone wrong. Maybe he was hit by an enemy's attack that was specifically designed to numb his senses. Another reason might be some kind of psychological trauma. For example, if he witnessed something extremely horrible, his mind might have shut down his ability to feel as a form of self - protection.
Maybe he's in a tight situation like being trapped in a small space or under some kind of magic spell.
Well, it could lead to some really tricky situations. For example, he might avoid certain missions near water or have to rely on his teammates more when water is involved. It could also be a source of embarrassment for him, like when his friends are having fun in the water and he has to stay on the shore.
One possible reason could be the loss of his friends. Naruto values his friends deeply, and if he were to lose someone like Sasuke again, it would be devastating. Another reason might be the pressure of being the Hokage. The responsibilities are huge, and he might feel like he's not living up to the expectations of the village. Also, memories of his lonely childhood could resurface, making him feel sad and alone, leading to him crying himself to sleep.
It might be due to hidden secrets. If there are dark secrets within Konoha that Naruto discovers in the fanfiction, such as a conspiracy that involves some of the higher - ups. This would make him lose trust in the village as a whole.
It could also be due to Sakura constantly doubting Naruto's abilities in the story. Naruto has always been looked down upon by many in the original series, and if in the fanfiction Sakura continuously expresses her lack of faith in him, it could lead to his unforgiveness. For example, she might have refused to believe in Naruto's new jutsu or his plans to save the village, which made Naruto feel really disappointed and unable to forgive her.
One possible reason could be a traumatic event. Maybe he witnessed something so horrible that it made him shut himself off from everyone. For example, if he saw his friends in great danger and couldn't save them in time, it might have led to his silence as a form of self - blame.
Perhaps he's under a powerful genjutsu. In the Naruto universe, genjutsu can manipulate a person's perception and behavior. It's possible that an enemy has cast a genjutsu on Naruto that makes him believe that if he talks to anyone, something bad will happen to them, so he chooses to remain silent.