A long-term (2002–2011), spatially robust, ichthyoplankton sampling program conducted in the New York/New Jersey Harbor produced 3,033 epibenthic samples from which the relationships between winter flounder egg and larval distributions and environmental parameters were examined. Variations in water temperature, sediment characteristics, and tidal phase were all significantly associated with egg distributions. Inferences about spawning habitats were based on the presence of early-stage eggs (ES1 and ES2). In the Lower Bay (LB), these habitats were primarily non-channel and characterized by more sandy substrates, averaging 96.5 % sand, 2.3 % silt/clay, 0.2 % total organic carbon (TOC), and shallower water (average depths of 5.3 m) compared to LB non-channel stations without ES1 and ES2 eggs (50.2 % sand, 42.0 % silt/clay, 2.1 % TOC, and 7.9 m depths). Occurrences of all stages of eggs in channels were associated with strong tides and severe cold winter water temperatures. These conditions increase the probability of egg transport from shallow spawning sites through increased vertical mixing (strong tides) and delayed development that prolongs the risk of displacement (cold temperatures). Yolk-sac (YS) and Stage-2 larvae were smaller in 2010 when spring water temperatures were highest. Overall, YS larval size decreased with warmer winters (cumulative degree-days for the month preceding peak YS larval collections, r2 = 0.82, p < 0.05). In all years, YS larvae collected in LB were smaller and Stage-3 larvae collected in channels were larger and possibly older than those from non-channel habitat. Because estuarine winter flounder populations are highly localized, adverse effects experienced during egg and larval stages are likely to propagate resulting in detrimental consequences for the year class in the natal estuary.