Small pelagic fish off the coast of Peru in the eastern tropical South Pacific (ETSP) support around 10 % of global fish catches. Their stocks fluctuate interannually due to environmental variability which can be exacerbated by fishing pressure. Because these fish are planktivorous, any change in fish abundance may directly affect the plankton and the biogeochemical system. To investigate the potential effects of variability in small pelagic fish populations on lower trophic levels, we used a coupled physical-biogeochemical model to build scenarios for the ETSP and compare these against an already-published reference simulation. The scenarios mimic changes in fish predation by either increasing or decreasing mortality of the model's large and small zooplankton compartments. The results revealed that large zooplankton was the main driver of the response of the community. Its concentration increased under low mortality conditions, and its prey, small zooplankton and large phytoplankton, decreased. The response was opposite, but weaker, in the high mortality scenarios. This asymmetric behaviour can be explained by the different ecological roles of large, omnivorous zooplankton and small zooplankton, which in the model is strictly herbivorous. The response of small zooplankton depended on the antagonistic effects of mortality changes as well as on the grazing pressure by large zooplankton. The results of this study provide a first insight into how the plankton ecosystem might respond if variations in fish populations were modelled explicitly.