When you have a lone noun then it would be kun, when there is no kun for the character there must be an on
Mountain has kun, so alone [ 山 - yama ]
Combinations of nouns and nounlike words usually turns them to on.
Combine [ 富士山 - fujisan ] - all on
But you also have [ 山道 - yamamichi ] - all kun
It is experience dependent.

In case of mountain i would say if the mountain is the last character it would be read with on and words before it probably too.
If mountain is not the last character and it is not a part of already combined word then probably kun, and characters after it probably kun too.

Dude above is right, best to learn words and you would subconsciously isolate all the on and kun readings as meaning the same thing dependent on combination over time like a nip kid. Then writing would be obvious.