Physical and biological variables affecting juvenile Pacific herring (Clupea pallasi) in Prince William Sound (PWS) from 1995 to 1998 were investigated as part of a multifaceted study of recruitment, the Sound Ecosystem Assessment (SEA) program. Though more herring larvae were retained in eastern PWS bays, ages-0 and -1 herring used bays throughout PWS as nursery areas. Water transported into PWS from the Gulf of Alaska (GOA) contributed oceanic prey species to neritic habitats. Consequently, variations in local food availability resulted in different diets and growth rates of herring among bays. Summer food availability and possible interspecific competition for food in nursery areas affected the autumn nutritional status and juvenile whole body energy content (WBEC), which differed among bays. The WBEC of age-0 herring in autumn was related to over-winter survival. The limited amount of food consumption in winter was not sufficient to meet metabolic needs. The smallest age-0 fish were most at risk of starvation in winter. Autumn WBEC of herring and winter water temperature were used to model over-winter mortality of age-0 herring. Differences in feeding and energetics among nursery areas indicated that habitat quality and age-0 survival were varied among areas and years. These conditions were measured by temperature, zooplankton abundance, size of juvenile herring, diet energy, energy source (GOA vs. neritic zooplankton), WBEC, and within-bay competition.