Five years of field, laboratory, and numerical modelling studies demonstrated ecosystem-level mechanisms influencing the mortality of juvenile pink salmon and Pacific herring. Both species are prey for other fishes, seabirds, and marine mammals in Prince William Sound. We identified critical time-space linkages between the juvenile stages of pink salmon and herring rearing in shallow-water nursery areas and seasonally varying ocean state, the availability of appropriate zooplankton forage, and the kinds and numbers of predators. These relationships defined unique habitat dependencies for juveniles whose survivals were strongly linked to growth rates, energy reserves, and seasonal trophic sheltering from predators. We found that juvenile herring were subject to substantial starvation losses during a winter period of plankton diminishment, and that predation on juvenile pink salmon was closely linked to the availability of alternative prey for fish and bird predators. Our collaborative study further revealed that juvenile pink salmon and age-0 herring exploit very different portions of the annual production cycle. Juvenile pink salmon targeted the cool-water, early spring plankton bloom dominated by diatoms and large calanoid copepods, whereas young-of-the-year juvenile herring were dependent on warmer conditions occurring later in the postbloom summer and fall when zooplankton was composed of smaller calanoids and a diversity of other taxa. The synopsis of our studies presented in this volume speaks to contemporary issues facing investigators of fish ecosystems, including juvenile fishes, and offers new insight into problems of bottom-up and top-down control. In aggregate, our results point to the importance of seeking mechanistic rather than correlative understandings of complex natural systems.