Many, if not most of the contributors to English Language and Usage are native speakers so we have spent a lifetime acquiring our vocabularies.
As to how we learn the subtleties of meaning one of the ways is by asking the people from whom we learned them, often our parents, but also from reading and hearing the words in context.
For instance we know that "replete with" means "full of" literally in the sense of being full of food but sometimes means other things metaphorically while "fraught with" means "full of" in the sense of being encumbered because we have read many sentences using both words where the context is clear. We know that a bucket cannot be either "fraught" with water or "replete" with water because we have not read sentences with that construction. If we read one we would know that its use was either erroneous or poetic.
The way you, as a student of English, can learn these subtleties is to read and listen to as much good English as you can and, when you find a word you either do not recognise or of the subtle meaning of which you are unsure, to think about it and compare it with other contexts in which you seen the same word.