Background/Question/Methods The interactive effects of warming and eutrophication on food web structure and dynamics have been suggested theoretically, but experimental evidence is lacking. We examined the effect of increasing temperature and nutrients on an experimental omnivory module where bacteria are consumed by the protist Tetrahymena pyriformis, and both are in turn consumed by an omnivore protist species, Euplotes sp. To do so, we used a factorial design including two temperatures (22ºC and 25ºC) and two nutrient levels (half- and full- strength media), resulting in four treatments with six replicates each. We recorded the density of both protist species using fluid imaging and measured bacterial biomass through optical density (OD600) daily (excluding weekends) for 16 days. Fluid imaging also provided trait measurements—such as body size and shape—for the protists throughout the experiment. We examined how temperature and nutrients individually and interactively influenced the ecological and phenotypic dynamics of all species in the food web. We used convergent cross mapping analysis to detect causal relationships between population dynamics and changes in protist phenotype over time to better understand the drivers of food web response under possibly antagonistic effects of temperature and nutrients. Results/Conclusions Our results reveal the joint effects of temperature, nutrient and phenotypes on food web dynamics. We found that temperature and nutrient both additively and interactively affected each species population dynamics. In contrast to previous studies, our results indicate that the joint effects of temperature and nutrient differ across trophic levels: simpler, additive effects occur at the base, while more complex, interactive effects, are increasingly prevalent at higher trophic levels. We also detected antagonistic effects of temperature and nutrients on the food web dynamics, as suggested by previous studies. Top-down and bottom-up effects changed little at higher trophic levels. However, temperature and nutrients interactively altered the top-down forces between bacteria and each of the protist consumers. Last, we found increasing effects of phenotypic dynamics of the protists consumers in mediating the food web responses in higher temperatures and higher nutrient conditions, suggesting possibly important roles of phenotypic dynamics in a polluted, warmer world. Our results stress the need to incorporate temporal phenotypic response to better understand species interactions and food web dynamics under environmental changes.