Here is how the article above describes the poor conditions at Hart Island that contributed to the deaths of hundreds of Confederates:
Hart Island (almost always incorrectly referred to as Hart's Island) is considerably larger than Davids Island. It, too, is located on Long Island Sound, slightly south of Davids Island, about twenty miles from the southern tip of Manhattan. It was acquired by the DeLancey family from the British Crown in 1774 and was farmed by a number of families until shortly before the Civil War. The owner at that time leased Hart Island to New York State for use as a military rendezvous, depot and training camp. The state turned it over to the Federal government in late 1861. In the summer of 1863 half of the island was designated as a prisoner of war camp and became, in a short time, one of the prison camps with the highest mortality percentage rates of all northern camps. The original camp was a stockade enclosing four acres and both prisoners and guards were housed in tents. Through the use of many of the arriving prisoners as laborers, wooden barracks were erected by March, 1864, not soon enough, however, for the prisoners to avoid the cold winter winds and storms that swept across the Sound. During the month of April, 1865, more than 3,400 prisoners were crammed into barracks, also called wards, in the camp. Each ward contained a hundred men. There were three rows of bunks and two men to a bunk. Since there were only twenty wards, the crowding must have been even worse than officially admitted. From April to July, 1865, 7% of the total prisoner population died. United States Army Medical Inspector George Lyman reported that "the largest portion of deaths occurred from chronic diarrhea brought with them [by the prisoners], and pneumonia, which began to appear a few days after their arrival....The men being poorly clad, the weather wet and cold, and the barracks provided with no other bedding than such as the prisoners brought with them, the pneumonia cases developed rapidly... increased probably, to some extent by the crowded and unventilated condition of the barracks." A steamboat the "John Romer", manned by the U. S. Army, made regular trips between Manhattan and Hart Island bringing prisoners to the island. Nothing has been found to show how the bodies of those who died there were moved to Long Island, but it is probable that this same steamer performed this task. The dead would be either landed at one of the piers that then stood in Flushing Bay or, more probably, brought back down the East River to the Brooklyn terminus of the Catherine Street ferry for transport to Cypress Hills.