"The wind was foul an' the sea ran high,
She shipped it green an' none went by".

or; "She shipped green water night & day"

Sailing in rough seas & taking water over the sides. Green water is water between land & the continental self - shallow water is green, water beyond the continental shelf is deep or blue water. Shipping water is never blue though.
Green hand in a new hand that can't yet hold on to what's in their stomach. Barry