Zooplankton and chlorophyll-a samples and associated hydrographic data were collected at approximately weekly intervals in the Peconic Bay estuary for most of the period between May 1978 and June 1979. Surface zooplankton samples were obtained by simultaneously-towed 73 μm- and 202 μm-mesh nets, and subsurface samples were collected with 505 μm-mesh nets. Zooplankton numbers and displacement volumes fluctuated widely throughout the year, with highest values in early spring and summer. Juvenile or adult copepods accounted for means of 90.0% and 85.0% of the animals recorded for the 202 μm- and 73 μm-net samples, respectively. The combination of Acartia tonsa and A. hudsonica adults+copepodids accounted for a mean of 81.4% of the zooplankton recorded for the 202 μm-net samples, and the combination of copepod nauplii, Acartia spp. adults+copepodids, Oithona colcarva and Parvocalanus crassirostris accounted for a mean of 82.7% of the animals recorded for the 73 μm-net samples. Copepod nauplii were the most abundant zooplankters collected in the 73 μm-net samples, and they were generally collected in higher numbers than the total number of animals in the 202 μm-net samples. During the colder months, late copepodids and adults of larger copepod species comprised greater proportions of the total zooplankton than during the warmer months when nauplii and copepodids of smaller copepod species were predominant. The ctenophore Mnemiopsis leidyi and the medusa Cyanea capillata also had periods of abundance during warmer months. Differences between numbers of larger zooplankters collected over different depth intervals or in successive replicate tows over the same depth intervals, reveal the likely effects of both vertical and horizontal patchiness. Comparisons of zooplankton numbers from the present investigation, which were obtained with relatively fine-mesh nets, with values from previous studies in adjacent waters which used coarser-mesh nets, suggest that many previous investigations have seriously underestimated the numbers of smaller zooplankters, particularly copepod nauplii.