After you receive the new quest from the captain go on the Krystal's deck to connect the water supply first.
On the right from the exit, near the now closed hold, you can find the end of the green narrow pipe. Zoom on the soft tube hanging from it. Start with moving the lever to the right (make the correct move with the mouse), the one that protrudes from the deck. Next, catch the end of the loose tube and put it into the said pipe (make the correct move with the mouse). Finally, secure the tube from popping out of the pipe by moving the lever back to the left.
Leave the ferry and head to the metal tower with the water tank on top of it which is next to you. Climb up the ladder and move the lever, on the left side of the tank, down (the one that comes out from under the pipe).
Go down and return to the ferry. Go to the quarterdeck and then to the bridge where you can find the captain standing next to the steering wheel. Speak with him - it turns out that after his infamous cruise with automatons he threw the ignition keys into the water. You must solve this problem.