The balance of stoichiometric traits of organisms is crucial for nutrient cycling and energy flow in ecosystems. However, the impacts of different drivers on stoichiometric (carbon, C; nitrogen, N; and phosphorus, P) variations of organisms have not been well addressed. In order to understand how stoichiometric traits vary across trophic levels under different environmental stressors, we performed a mesocosm experiment to explore the impacts of warming (including +3 °C consistent warming above ambient and heat waves ranging from 0 to 6 °C), eutrophication, herbicide and their interactions on stoichiometric traits of organisms at different trophic levels, which was quantified by stable nitrogen isotopes. Results showed that herbicide treatment had no significant impacts on all stochiometric traits, while warming and eutrophication significantly affected the stoichiometric traits of organisms at lower trophic levels. Eutrophication increased nutrient contents and decreased C: nutrient ratios in primary producers, while the response of N:P ratios depended on the taxonomic group. The contribution of temperature treatments to stoichiometric variation was less than that of eutrophication. Heat waves counteracted the impacts of eutrophication, which was different from the effects of continuous warming, indicating that eutrophication impacts on organism stoichiometric traits depended on climate scenarios. Compared to environmental drivers, taxonomic group was the dominant driver that determined the variations of stoichiometric traits. Furthermore, the stoichiometric stability of organisms was strongly positively correlated with their trophic levels. Our results demonstrate that warming and eutrophication might substantially alter the stoichiometric traits of lower trophic levels, thus impairing the nutrient transfer to higher trophic level, which might further change the structure of food webs and functions of the ecosystems.