Either Lewis or Clark had mental health issues, which one was it, and what was the issue?
That would be Captain Meriwether Lewis. Keeping in mind the historical difficulties of psychologically diagnosing someone long after their death, Lewis' long bouts of depression were well known and documented in diaries, letters and journals, and he had experienced them since the time of his youth. Dr. Benjamin Rush wrote to President Thomas Jefferson and expressed concern about his ability to handle the expedition.
In those days, little was known about the fairly common mental malady, and Lewis himself referred to it simply as "blue periods".
Lewis had a hard time dealing with it, and was likely bipolar. The commonly accepted version of events is that, despondent over family deaths, accusations of corruption during his Governorship of Louisiana and his financial situation, Lewis took his own life with a pistol, although his family and some historians still believe he was murdered.