The ecologic and stratigraphic development of the lower Hudson River estuary during late Pleistocene time was reconstructed from foraminifers and pollen in cores taken from Peekskill, New York, to The Narrows of New York Bay. Sediments deposited in freshwater, brackish water, and marine environments were penetrated by the cores, which ranged from 32.0 to 72.7 m. The foraminifers identified in the cores are divided into four assemblages, each characteristic of a local stratigraphic zone and biotope. Three of the assemblages currently thrive in the estuary; the fourth, composed primarily of benthonic foraminifers, is now found on the nearshore continental shelf from Portsmouth, New Hampshire, to Cape Hatteras, North Carolina, and in easternmost Long Island Sound. Spruce-fir, pine, and oak pollen assemblages occur in the cores and are zoned using the standard pollen zones established for the northeastern United States. The pollen zones are used for chrono-stratigraphic purposes. Following the dissipation of glacial Lake Hudson, tidal conditions were established in the estuary well before 12,000 yr ago. Estuarine conditions with salinities high enough to support foraminifers became established by ∼11,500 yr ago. About 10,000 yr B.P., salinity decreased slightly but was re-established by 9,000 yr ago. The maximum transgression of mesohaline brackish water into the estuary occurred about 6,500 yr B.P., as shown by the first appearance of foraminifers in the northern part of the area. This event correlates with the general flooding of the northeastern United States by the Atlantic Ocean. The areal distribution of foraminiferal biofacies in the estuary 6,500 yr ago indicates the maximum limit of mesohaline water in the Hudson River Valley during postglacial time. Foraminiferal evidence indicates that the salinity of the estuary has decreased during the past 1,500 to 3,000 yr. This is the result of sediment being deposited faster than sea level rises or the crust subsides, so that the salt-water wedge within the estuary is regressing oceanward.