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Tropical reservoirs in China receive a high input of organic matter from surrounding watersheds and this represents a significant resource for zooplankton consumers. Copepods are often the dominant zooplankton group in the tropical systems. Whether copepods tend to be omnivorous and their potential cascading effect on phytoplankton are subjects of debate. We used stable carbon and nitrogen isotope analyses to elucidate the allochthony and trophic positions of two copepod species (Phyllodiaptomus tunguidus and Mesocyclops thermocyclopoides) and one cladoceran species (Diaphanosoma orghidani) over a one-year period in a tropical oligo-mesotrophic reservoir in China. We assumed the filter-feeding D. orghidani was herbivorous and we used it as a baseline indicator of δ15N to estimate the trophic position of the two copepods. P. tunguidus and M. thermocyclopoides had an average trophic level that was 0.7 and 0.5 higher, respectively, than that of D. orghidani. M. thermocyclopoides showed seasonal differences in trophic position and an increase in trophic position with rising temperatures, whereas P. tunguidus remained omnivorous throughout the year. All three zooplankton species had a much higher degree of allochthony in the flood season than in the dry season, and their allochthony was positively related to the allochthony of the particulate organic matter input. The two copepods’ omnivorous behavior suggests their allochthony was primarily linked to microbial food web based on the input of terrestrial organic matter. The chlorophyll a to total phosphorus ratio was much higher when P. tunguidus dominated the zooplankton community than when D. orghidani dominated. The ratio was positively related to the ratio of omnivorous adult copepods to cladoceran biomass but not to the zooplankton:phytoplankton biomass ratio. Our results suggest that copepods tended to be omnivorous and relied heavily on allochthonous material in the study reservoir. The indirect cascading effect is likely to be stronger than the direct grazing effect, resulting in a positive effect of copepods on the phytoplankton.