Both Journal and diary have etymology of "day" and basically mean the same thing.
Journal from the French (jour)
Diary from the Spanish/Latin (diario)
But in common usage, a journal is synonymous with "log"; that is, it is a chronicle of events. An example of this is the Journal of the American Medical Association, or JAMA. A diary is more-or-less used exclusively for emotions, feelings and what have you and is usually addressed with "Dear Diary" and written to as if it were a person. An example, "Dear Diary, today I fell in love with Marilyn. She's cute, isn't she?"
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