© 2022, The Author(s), under exclusive licence to Springer Nature B.V.Autochthonous and allochthonous organic carbon (OC) are important carbon sources for zooplankton in lakes, and changes in the abundance and proportions of those sources may affect zooplankton community composition and lake ecosystem function. Nevertheless, long-term changes in assimilation of autochthonous and allochthonous carbon by zooplankton and associated climate- and environment-related forcing mechanisms have rarely been studied. We used a sediment record of cladoceran remains and geochemical variables from Lake Jirentso on the Tibetan Plateau to track long-term changes in sources of carbon for cladocera over the past ~ 950 years. High cladoceran:diatom accumulation rate ratios during the cold Little Ice Age indicated that cladocerans assimilated more allochthonous OC that was released from glaciers and frozen soils to replenish their food supply, a consequence of low primary production in the lake. In contrast, low cladoceran:diatom accumulation rate ratios during the Current Warm Period indicated that cladocerans utilized more autochthonous OC. Less autochthonous OC was available for cladocerans during the Medieval Warm Period than during the Current Warm Period. The total accumulation rate of cladocerans was significantly correlated with the annual mean air temperature, total phosphorus, and the organic carbon to nitrogen ratio in the sediment core. Recent warming and sharply increased nutrient inputs affected the cladoceran and diatom assemblages, further inducing a shift in the diet of zooplankton towards more recently produced OC. The sediment record from Lake Jirentso, which represents the last ~ 950 years of deposition, spanned an ideal time window for assessing historical changes related to the impacts of climate and nutrients on zooplankton carbon sources.