The influence of seasonality of the aquatic environment on food web has been notoriously understudied in empirical ecology. In this study, we focus on seasonal changes in one key attribute of a food web, the trophic level. We determine whether seasonal variations of fish trophic levels could be indicated by the change in food resources. Silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) were used to explore the responses of trophic levels of the filter-feeding fish to seasonal variations of food resources. Combined stable isotopic analysis and dietary analysis revealed that filter-feeding fish tended to have a higher trophic level in spring (May) and autumn (September and October). This may result from the abundant density of food resources (zooplankton and phytoplankton) and fish flexible foraging strategy, as we predicted that the trophic level follows the seasonality of food availability. Pearson' correlation analysis and a structural equation model showed that seasonal variation of total phosphorus and water temperature could indirectly affect trophic levels of silver carp and bighead carp by mediating the abundance of phytoplankton and zooplankton directly and indirectly along the food chain. According to these findings, the seasonal variation of food resources could be an important indicator of the temporal dynamics of the food web trophic pattern in freshwater ecosystems.