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The British took so many prisoners during the Revolutionary War that they quickly ran out of space to hold them all. Prisons in New York (like the Bridewell) were full and the British took to using sugar houses, and pro-rebel churches in the city.
In the harbor, decommissioned war ships were put to use as prison ships, the most well-known being the HMS Jersey. The Jersey had – and earned – the nickname 'Hell'. Conditions below decks (where the prisoners were kept) were crowded – a thousand men crammed together without light, sanitation, or proper ventilation.
About a dozen prisoners died every day – from smallpox, yellow fever, malnutrition, and torture by the guards. The British sentiment was that the rebels were traitors and didn't deserve any better.
At least 11,000 people died on board prison ships – more that the rest of the war put together. After the British left New York, the US Navy found mass graves in the mud at the edge of the harbor. Those remains have since been placed under a monument in Brooklyn, where Fort Putnam used to be.