In a word: nope. "Go in over your head" just doesn't fly. In your example, "got in over my head" is a perfect fit.
Of course, there's also the expression "to go over one's head", which is completely different but may create some confusion. It means something is too complicated for someone to understand. "Quantum physics goes over my head, as much as I would love to understand the basics."
The toughest thing of any language is its idiomatic expressions. They often make no sense, and follow no logic whatsoever. They assert their own rules. We learn them by ear and use them impulsively. They defy close scrutiny.
No clue why they are the way they are. It's a head scratcher. Must be that each refers to some long-forgotten, well publicized story. Say some famous figure misjudged his/her swimming prowess and got taken down a peg during the rescue. Undoubtedly, as usage of a newly minted phase "ha ha! Help me never get in over my head like Pat did" spread to the masses, the cognoscenti would nod when they heard it, smiling because they knew just the incident that had given life to this new expression. People misusing it simply revealed their own ignorance.
Or at least I guess some reason like that is behind the stubbornness we feel about word choice and usage when it comes to these colloquialisms. We're bound by unwritten laws when we trot out such fanciful turns of phrase.
But wait: their misuse can actually be powerful. Breaking the laws purposefully and cunningly can reinforce the notion you are expressing. Breaking them clumsily will distract from your intent. It may not be time to give up on your idea, and to risk going in over your head.