They sank in water.
The pirates main problem, as I understand it, was that the human body lacks the ability to process and utilize the oxygen in the water that surrounded them as they sank. If they had had some appropriate equipment, like scuba gear or a submersible device, they might have been able to get around the sinking problem. But hey, they're pirates, and they don't always think things through. Aaargh.
The dreaded killer......dihydrogen monoxide!