Just south of the lighthouse is one of Riddler's puzzles. This one is a bit tricky. First, use the Batmobile winch to pull out a concrete slat. Hop out, apply some Explosive Gel, hop back in, and return the slat to its original position. Detonate the gel to destroy a pump inside, clearing out the harmful steam at the end of tunnel. Now pull the slat back out of the way, and do a running slide through the small opening, past the shut-off valves, and into the container. The trophy is all yours!
Just south of the previous trophy is another puzzle, down in a ditch. This one works a bit like pinball. Use the winch to pull back and release the block to launch the trophy ball. A few launches will get it into the prize slot, where you can pick it up.
There's a small building below Merchant Bridge. Drop down to find a trophy by a beach chair on the roof.
Falcone Shipping Antenna
Check the southern edge of the facility to find another puzzle. Use the Batmobile winch to pull the train forward, taking it off a grate. Head back there and slip into the grate to find a trophy underneath.
Warehouse near Mercy Bridge
Check just on the east side of the Bleake Island side to find a Riddler puzzle inside a warehouse. This is one is kinda tough. First use the Batmobile winch to pull down the wall of questions marks. Next, you need to shoot each one as it passes under the rings along the wall. It may take a few tries - make sure you hit the center mark last - but doing so will net you another trophy.