We reported diel fluctuation in isotopic composition of surface seston from two connected lakes in China, oligotrophic LakeFuxian and eutrophic Lake Xingyun. The decrease in nighttime and the increase in daytime of isotope signatures of seston mightbe attributed to the light-dependent balance between the photosynthesis and the respiration of phytoplankton and to the changesin the species composition and the relative abundance of phytoplankton functional groups at the water’s surface in diel growth.The relatively high isotopic signatures and the large-extent diel fluctuation of phytoplankton in the eutrophic lake could be dueto utilization of heavy-isotope-enriched inorganic sources and the high primary productivity. Extent of diel fluctuation in δ13Cand δ15N of phytoplankton were relatively small compared with the isotopic enrichment per trophic transfer and thus might havenegligible effect on the source identifi cation and the trophic evaluation of consumers.