Climate warming and eutrophication caused by anthropogenic activities strongly affect aquatic ecosystems. Submerged macrophytes usually play a key role in shallow lakes and can maintain a stable clear state. It is extremely important to study the effects of climate warming and eutrophication on the growth of submerged macrophytes in shallow lakes. However, the responses of submerged macrophytes to climate warming and eutrophication are still controversial. Additionally, the understanding of the main pathways impacting submerged macrophytes remains to be clarified. In addition, the influence of seasonality on the growth responses of submerged macrophytes to climate warming and eutrophication requires further elucidation. In this study, we conducted a series of mesocosm experiments with four replicates across four seasons to study the effects of rising temperature and nutrient enrichment on the biomass of two submerged macrophytes, Potamogeton crispus and Elodea canadensis. Our results demonstrated the seasonality and species specificity of plant biomass under the influence of climate warming and eutrophication, as well as the main explanatory factors in each season. Consistent with the seasonal results, the overall results showed that E. canadensis biomass was directly increased by rising temperature rather than by nutrient enrichment. Conversely, the overall results showed that P. crispus biomass was indirectly reduced by phosphorus enrichment via the strengthening of competition among primary producers. Distinct physiological and morphological traits may induce species-specific responses of submerged macrophytes to climate warming and eutrophication, indicating that further research should take interspecies differences into account.