Winter flounder habitat use in New York/New Jersey Harbor was examined through a long-term (2002–2010) bottom trawl sampling program (Aquatic Biological Survey) in which 5234 winter flounder were captured in 2069 samples collected at approximately 26 stations throughout the harbor. Interannual variability in catch-per-unit-effort (CPUE) primarily was attributable to fluctuations in Year-1 juvenile CPUE, which was positively correlated with total annual egg abundances from the previous year. Adult male CPUE during the spawning season was positively correlated with total egg abundances of the same year, whereas adult female CPUE was unrelated to annual egg abundances in the harbor. Annual variation in adult male densities in the harbor during the spawning season reflects the intensity of estuarine spawning activity, whereas adult female densities may include non-reproductive, foraging individuals. Seasonal fluctuations in condition indices reflected energy use during the spawning season, with relatively high condition in January, reduced levels in March and April, and elevated condition again in May. Adult CPUE peaked in April, coincident with the critical feeding period that follows spawning. Mean April water temperatures were positively correlated with egg abundances the following year and Year-1 juvenile CPUE two years later. A similar correlation between April temperatures and Year-1 juvenile abundances two years later was demonstrated using published data for winter flounder collected in Niantic Bay, CT. Higher April water temperatures may enhance benthic secondary production during the critical feeding period, and thus increase prey availability for foraging adults that need to restore energy reserves in order to reproduce the following year. A direct examination of benthic secondary production and variation in winter flounder estuarine foraging and subsequent spawning activity is needed to more fully understand this relationship.