With nothing to curb their fertility, the original horses proliferated and overgrazed the marsh grasses. This unbalanced the estuarine ecology and weakened the whole food web supported by the marsh. Feral horses also interfered with nesting birds, some of them rare.

By 1986, the equine population on this small island had reached 68. There simply wasn't enough food for all of them. Mother Nature handled the overpopulation problem in her own way during the winter of 1986-1987. Famine and parasites presumably killed twenty-nine individuals within a few short months. (Nineteen bodies were found, and ten horses remained missing and were presumed dead.) Once concerned locals realized what was happening, hay was brought in as supplementary feed. The starving horses, used to consuming only native grasses, mostly ignored the hay.

By August, 1988, with numerous births, the herd numbered fifty-one. The NC division of Marine Fisheries had helped them through the 1987-1988 winter by providing twenty bales of hay each week to help nourish them. A point well was also dug to ensure a fresh water source. But clearly this human assistance could not continue. If the horses were to remain on the island, their numbers had to be be reduced to put them back in balance with their environment. It was determined that the island could comfortably sustain between fifteen and twenty-five horses, and in 1988, the state removed thirty-three of the fifty-two horses from Carrot Island. Nine of them tested positive for equine infectious anemia and were euthanized. The remainder were adopted by private citizens. In 1996, the population was up to thirty again, and a dart-gun birth control program was initiated for both mares and stallions.