I can't tell you how many people I've watched fail at Japanese. It doesn't matter if they were fellow students I learned alongside, students I taught or tutored, people who I've talked about Japanese with in some way, or even other Japanese scholars and teachers, there are people who really struggle with the language and can't speak or hear the language naturally for the life of them.
And so often, they're all making the same mistake: they are translating between Japanese and English in their head.
It sounds counter-intuitive -- isn't a major point of learning a second language so you can translate it? Yes, this is true, but translation is an applied skill, and it's something you can only do once you already understand two languages fully. Translation is not the way you should be learning your languages, though.
While it should go without saying, Japanese is not English. And I don't just mean the sentence structure is different, and I'm not just referring to how there are certain concepts or words that don't really translate. I mean nothing at all directly corresponds to something in English, not even concrete nouns, and you shouldn't think of it that way.
Think about how you expand on your native language. When you learn new things about English, you're learning new language, even though you've already lost your ability to pick up a native language. Of course, it's easier than learning a second language because it conforms to a paradigm you know well, but you're still learning something completely new.
The World Wide Web did not exist when I was born, nor by the time I had lost the ability to learn native languages. However, I still know words like "website," "hypertext," and "URL." How did I learn these? I certainly didn't translate them through another language. Though, I did learn about them through English. I learned that a website is that 'thing you can go to online with a bunch of webpages' and that hypertext is 'interactive text that links text to other text or media' or whatever. It wasn't translated from some other language in which I already knew those words. I had to learn them as concepts.
This focus on concept is what's important here.
You should be learning Japanese, or any language, through concept, not through translation.
And do this with everything, not just the confusing things.
Learn new words they same way you would learn them in English, so that you understand them in the same way you understand English words.
Imagine if I asked you to tell me what a refrigerator was. Pretend I really didn't know at all, like I'd never even seen one before. But the only language I know is English. How would you explain it to me? Would you just say el refrigerador and expect this Spanish translation to suffice? Of course not.
You'd describe the concept to me. There are a ton of ways you could do it -- perhaps you'd say 'It's a big cold box you put food in' or you might be more technical and say it's an electrical appliance used for chilling objects, particularly edible ones. Or maybe you'd even take me to your own fridge and show it to me and explain how it works hands-on.
And then I would know what a refrigerator was, and I would not have used translation at all.
Words are stored in your brain in something we call "lexicon." You access your lexicon through concept -- when you imagine that big cold box with food in it, your brain connects to the entry in your lexicon that knows that that thing is called a 'refrigerator.' The more experience you have thinking about it in various ways (talking about it, using it, whatever), the faster and easier your brain will be able to access the lexical entry. Similarly, when you hear the word 'refrigerator,' your brain accesses that entry and you think about the idea of a refrigerator.
When learning Japanese, or any second language, you need to build onto your lexicon, not just learn translations.
When you learn a new word in Japanese, chances are you're going to learn it through translation. For example, if you want to know how to refer to "dog" in Japanese, you will look it up in a dictionary or ask a Japanese friend or something. And you'll get a one-word response:
犬 (いぬ inu)
If you just learn this like you would learn a science fact or piece of trivia "OK, 'inu' means 'dog,' " then you have not created a lexical entry for this word in your head. Your brain is not processing this the way that you process normal language. It's just learning some random fact. So now if someone asked you "Can you translate 'dog' into Japanese?" then, if your memory serves you well enough, you'll be able to come up with 'inu.' But that's not speaking a language; that's just reciting trivia.
Imagine you look out your window and there is a dog in your yard. You don't have a pet dog so this is a bit of a surprise. You want your friend to look at the dog too. So you say "Look! A dog!"
Now, when this happens, you don't translate "Look! A dog!" from some mystery language into English. You have this concept in your head -- there is this canine animal within your sight, and there's another person around, and you want to encourage them to also bring this animal into their sight. This concept is in your head, and your lexicon naturally accesses the words for you so you can say them.
Now, if you wanted to say this in Japanese, but all you ever did was learn "inu means dog in Japanese," you don't have this lexical access. Your brain won't naturally pick those words for you. It will instead just pick the English words, because that's all it knows.
Now you have to go through the trouble of translating it in your head, which is work, and it will produce a result, but it's not the same as speaking a language naturally.
Imagine if you were speaking Japanese with a friend who didn't know English at all, and they knew you were a computer expert, and they asked you to explain the concept of cloud computing to them.
Having to translate in your head is like having to sit down with a piece of paper and work out an algebra problem. If the problem is simple enough, you can do it in your head, and spit out an answer, but the more complex it is, the harder it's going to be. Eventually, you just won't be able to do it. People who learn Japanese through translation speak choppy, broken Japanese because their brain is literally incapable of producing the language naturally. Putting together a complex idea into words is too hard, because their brain can't process it, so they say a bunch of smaller ideas or chunk together things that don't make sense. Likewise, they have trouble understanding Japanese when they listen to others speak because they get bogged down trying to translate in their head. They miss a lot of nuances, syntax structure, and even entire words and phrases, because their brain can't keep up.
What you need to do is, after you see in the dictionary that inu = dog, is to ignore that relationship between the Japanese and English words. Instead, think of all kinds of different things about dogs. Imagine your own pet dog or a friend's dog, and imagine yourself referring to it as inu. Think about pet shops, dog training facilities, dog houses with dogs in them, puppy calendars, think about all kinds of dog things, and think to yourself 'this is inu.'
The concept of that creature that you're thinking about should become inu to you. The idea that inu is dog should not be as natural.
You can even try it now! Think about the season of summer. Now, forget about the word itself. What are you thinking about? You probably have a certain picture in your head. Maybe a scene from childhood, or your favorite vacation spot, or a certain holiday or event, or something. Think about that image. Think about all the things you associate with that time and that image -- maybe it's ice cream, or the beach, or hanging out with your friends, or visiting your family. Maybe you think of ideas that aren't so concrete, like the heat. Just think about all those things. Don't think of any words. Just ideas.
Let's add some ideas to that. In Japanese culture, some popular imagery associated with this season is the loud cry of cicadas, and smashing open watermelons on the beach. Mix those with the ideas you were already thinking about.
In Japanese, this season is called 夏(なつ natu/natsu). Without thinking about the English word, apply this new Japanese word to the ideas in your head. Know that the way to refer to this season is natsu.
If you want to try more, but without the prompting from me, try to go from these dictionary translations to your own lexical entries that link Japanese words with ideas for the other four seasons:
春(はる haru) - spring
秋(あき aki) - autumn
冬(ふゆ fuyu) - winter
Translation, as a skill, comes after you do learn another language like this. You hear about an idea in one language, then think of the idea, then express it in a new way in another language. Sometimes, if you were to use a dictionary, it would sound completely different! This is why computer translations always make no sense (and even when they do make sense, they're usually wrong!) because the computer cannot process ideas, it can just link up words to translations. If you learn Japanese, through translation, your Japanese will literally sound like Google Translate, and when you hear Japanese, you'll interpret it like that and just be trying to guess what it means.
As you continue to learn Japanese, you'll start to realize that even the most basic things don't really 'line up' with English anyway. Dictionaries are rough estimate of what the most similar words are between languages. Translation, though, is completely made up. When Japanese was created, it was not based on English, and when English was created, it was not based on Japanese. So no word came about in the same way. There may be something you look at at say "table" in English, but a Japanese person might say 机(つくえ tukue, tsukue) which in a dictionary will say "desk." Learning these nuances is up to experience, just as it is in learning words in your native language, and if you're using translation to learn, you'll never be able to do it.
It will take a little bit of effort to overcome the tendency to want to 'translate' things as you learn them, but soon it should become second nature. You'll have to use English to learn about Japanese, but you should be using concepts and ideas to actually learn Japanese. You can do this from your very first word you ever learn in Japanese, and should never look back to memorizing translations ever again.
If you've already come so far and have been learning through translation, try to relearn as much as you can. Think about the concepts when you think about words, rather than their English 'equivalents.'
The more you learn Japanese, the more you brain will separate your Japanese and English lexicon, and the less you'll think about them jointly. Your brain will switch between 'Japanese mode' and 'English mode' when it needs to, and when you are 'thinking in Japanese,' the English words won't even come to you unless you make an effort to think of them.