The Peconic Estuary, at the eastern end of Long Island, has been plagued by a recurrent algal bloom, locally referred to as ?Brown Tide,? that has caused the severe decline of local marine resources. Although the factors that trigger Brown Tide blooms remain uncertain, groundwater discharge has previously been shown to affect surface-water quality in the western part of the estuary. A U.S. Geological Survey groundwater- flow model of the main body of Long Island indicates that a total of about 7.5 x 106 ft3/d (cubic feet per day) of freshwater discharges to the western part of the estuary, but the model does not include the ground-water flow systems on the North and South Forks and Shelter Island, which contribute significant amounts of freshwater to the central and eastern parts of the estuary. The need for information on freshwater discharge to the entire estuary prompted the U.S. Geological Survey to evaluate ground-water discharge from the North and South Forks and Shelter Island. Source areas that contribute ground water to the Peconic Estuary were delineated, and groundwater budgets for these areas were developed, to evaluate the distribution and magnitude of ground-water discharge to the central and eastern parts of the estuary. Contributing-area boundaries that were delineated coincide with the hydraulic boundaries of the fresh ground-water-flow systems of the North and South Forks and Shelter Island; these boundaries are of two types? external (saltwater bodies) and internal (groundwater divides). Hydrologic components that were evaluated include recharge from precipitation, public-supply withdrawal and return flow, and agricultural withdrawal. Values for each of these components were calculated or estimated for the individual freshwater flow subsystems that form each ground-water-budget area, then summed to obtain the total discharge of fresh ground water to tidewater. Ground-water discharge to the Peconic Estuary is about 3.8 x 106 ft3/d from the North Fork, 11 x 106 ft3/d from the South Fork, and 1.7 x 106 ft3/d from Shelter Island. The total contribution to the estuary from these areas is about 16 x 106 ft3/d?roughly twice the total contribution from the main body of Long Island. In contrast to the freshwater contribution from the main body of Long Island, which is concentrated near the head of the estuary, the contributions from the North and South Forks and Shelter Island are distributed along the east-west length of the estuary. Changes in water-table altitude and the resulting changes in total discharge to the Peconic Estuary were estimated from the relative changes in annual mean water level at observation wells. The 1985-95 interval included 7 years (1985-88, 1991- 92, 1995) of generally below-average water-table altitudes that presumably caused similar decreases in ground-water discharge to the estuary; intense Brown Tide blooms coincided with six of these years (1985-88, 1991, 1995), and localized blooms coincided with the remaining year (1992). Watertable altitudes in the remaining 4 years of the 1985-95 interval (1989-90, 1993-94) were nearly average or above average, and presumably produced comparably near-average or increased amounts of ground-water discharge to the estuary; none of these years saw any widespread Brown Tide blooms. Fluctuations in the amounts of ground-water discharge to the estuary appear to affect the occurrence of Brown Tide blooms, although the factors that trigger the blooms have not been determined.