Depth of marsh sediment was probed throughout Jamaica Bay islands including Jo Co Marsh, Silver Hole Marsh, Big Egg Marsh, Little Egg Marsh, Yellow Bar Hassock, and Stony Creek Marsh. All of the marshes are underlain at depths of 2 m or less by sand. Two cores were analyzed for pollen and macrofossils. The easternmost core, from JoCo Marsh, was comprised of 2 meters of marsh peat atop .86 meters of sand while the western bay core, from Yellow Bar, was comprised of 1.9 m of peat atop sand. Sandy, shallow pools characterized the present-day JoCo marsh environment about 2000 years ago. Foraminferal species such as Elphidium were dominant. Preservation of killifish scales indicate that this area was probably a low-energy environment, similar to shallow pools where killifish enter Jamaica Bay today. Salt marsh peat accumulated, and Trochammina spp. became the dominant foraminiferal type, followed by other marsh species such as Milliamina and Rotamorphina. Regional vegetation shows a dominance of Pinus (pine) forest compared with Quercus (oak) today, possibly signaling a Little Ice Age response. The subsequent rise in Ambrosia (ragweed) reflects the forest destruction and the open environment that resulted as Europeans colonized the region. It is only in the uppermost sediments (30 cm) that Salicornia seeds are continuously present, suggesting more saline conditions. The last century shows a resurgence of the Quercus-Pinus forest after the decline due to early European influence.