Obviously Bongo Bongo the Phantom Shadow Beast (and boss of the shadow temple.) is a man who got executed by getting his head and hands chopped off and his spirit was imprisoned there by Impa so he couldn't wreck havoc upon the village.
Now, think of what the old man in Kakariko village about a man said to have created an item enabling its user to "see the truth", later revealed as the Lens of Truth. The creator of the Lens of Truth (thought to be a sheikah.) resided where the Kakariko well now stands. With all this evidence it is said that Bongo Bongo may be the creator of the lens of truth. Though if the Lens of Truth creator and Bongo Bongo are the same person is still up to debate, I think it is obvious (to me at least.) that its true.
Sorry if you think is short but if I added the whole Sheikahs and Shadow Temple like I originally planned to it would be too long.