In natural systems, a multitude of environmental stressors can interactively influence wildlife phenotypes. Understanding the patterns in phenotypic changes under multiple stressors is key to identify the principles in relationships between traits and phenotype–environment associations. In the present study, we examined the changes in fitness‐related parameters (somatic growth, fecundity, survival and population growth), and expression patterns of three phenotypic responses (hemoglobin production, enlargement of filter‐screen area and neck teeth formation) in the freshwater zooplankton Daphnia pulex, by rearing their individuals under factorial combinations of three environmental stressors (oxygen deficiency, food limitation and presence of kairomones released from Chaoborus spp.). Changes in the fitness parameters indicated the presence of trade‐offs with energy allocation between life‐history traits and phenotypic changes. The hemoglobin expression level was enhanced not only by low oxygen conditions but also by presence of the kairomones, however, it was reduced under low food conditions. Interactive effects of multiple stressors on morphological changes were also detected: the development level of neck teeth was reduced under low oxygen conditions, and the filter‐screen adaptation under low food conditions was also slightly suppressed by exposure to the kairomones. Various ecological situations can interactively determine the phenotypes, affecting population dynamics and consequent community structures through the modification of biological interactions.