Why does my 17 foot Carolina skiff with no visible hull damage get water inside when in use but not while setting empty at dock?

Either water is getting in over the gunwales when in use, or there is a leak, however small, above the unladen waterline.

I would suggest loading it with a series of weights (concrete blocks or bricks), so that you progressively raise the waterline, and then see where that level is at when water is getting in.