If someone is “in over their head” it means that they are in a situation that is too difficult for them to handle properly. The original idea of the phrase is talking about someone who can’t swim, but is swimming in deep water.
They need to be saved because the water level is “taller” than them. If no one helps, they will drown because their feet can’t touch the bottom. I think you understand the main idea.
Some real examples:
1. Some people think that Obama is a great president; other people think he’s in over his head in terms of dealing with the US economy. (It doesn’t mean he’s stupid, it just means it’s too difficult for him to deal with properly)
2. He made his resume sound really amazing. It helped him to get a great new job, but now he’s in way over his head. His boss is expecting a lot from him and he has no idea what to do. He’s super stressed!
That was a short and simple lesson. I hope it was quite helpful