EcoSim II uses results from the Ecopath procedure for trophic mass-balance analysis to define biomass dynamics models for predicting temporal change in exploited ecosystems. Key populations can be represented in further detail by using delay-difference models to account for both biomass and numbers dynamics. A major problem revealed by linking the population and biomass dynamics models is in representation of population responses to changes in food supply; simple proportional growth and reproductive responses lead to unrealistic predictions of changes in mean body size with changes in fishing mortality. EcoSim II allows users to specify life history mechanisms to avoid such unrealistic predictions: animals may translate changes in feeding rate into changes in reproductive rather than growth rates, or they may translate changes in food availability into changes in foraging time that in turn affects predation risk. These options, along with model relationships for limits on prey availability caused by predation avoidance tactics, tend to cause strong compensatory responses in modeled populations. It is likely that such compensatory responses are responsible for our inability to find obvious correlations between interacting trophic components in fisheries time-series data. But Ecosim II does not just predict strong compensatory responses: it also suggests that large piscivores may be vulnerable to delayed recruitment collapses caused by increases in prey species that are in turn competitors/predators of juvenile piscivores.