In the early 1980s, the New York State Department of Environmental Conservation (NYSDEC) began the development of a fishery-independent trawl survey program to monitor and assess local populations of weakfish (Cynoscion regalis) in the Peconic Estuary. The project was initiated based on the research recommendations of the Atlantic States Marine Fisheries Commission’s (ASMFC) Fishery Management Plan for Weakfish (Mercer, 1985). Gear and methodology for this survey were finally standardized in 1987 after 3 years of trials, and the official dataset for this survey begins in 1987. The initial intent of the survey was to develop an annual index of recruitment of juvenile weakfish and determine the relationship between spawning stock and environmental factors on year-class strength for weakfish. Although this survey was designed to study juvenile weakfish, due to the diverse number of species in the Peconic Estuary, data collection was expanded to include identifying and measuring all species of fish, as well as squid, horseshoe crabs, and mantis shrimp. Species of macroinvertebrates are identified and counted (Weber, Grahn, and Havens, 1998). As of 2019, certain macroinvertebrates (calico crabs and whelk species) are being measured as well to provide more data in efforts towards conservation and management of those species. While many of the species encountered in the trawl may not themselves be directly important to New York’s recreational and commercial fisheries, some of these species are significant as forage or bait species (e.g. Anchovies, Herring, Silversides), as well as providing insight into the ecological relationships among these species and their significance as indicators of the health and well-being of this important estuary. The catch per unit effort (CPUE) measures the quantity of fish caught during one tow of the trawl. This is used to estimate the abundance of fish in a population. This dataset includes the average CPUE by species and year.