It must be complicated for learners, I’m always feeling really sorry for the illogical difficulties they face up to. 
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There are two different types of phonetical expressions for most of all 漢字.
The first type ‘Kun’ is derived from the indigenous Japanese lexicon(やまとことば). The word ‘Sakana’, for example, is in this type.
The second type is ‘On’, and it is derived from Chinese lexicon. The words ‘Nin’ and ‘Gyo’ are both in this type.
Normally we don’t mix these two types of sounds in one word. Say, a ‘Mermaid’ is naturally a one word, I mean it is one abstract idea. Thus we pronounce both characters 人 and 魚 with On-type sounds.
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Actually this is a totally abridged explanation, so there must be more and more questions emerging throughout your learning. But my knowledge isn’t sufficient enough to explain it thoroughly.