ong-term trends, spanning about 150 years, in δ13C values in the head capsules (HCs) of three chironomid taxa and pelagic cladoceran exoskeletons are reported for a reoligotrophicated, deep, clear-water lake using a multidepth approach. The trends were taxon specific, and Bayesian change point analyses defined three homogenous temporal sequences of HC δ13C. From the 1850s to the 1930s, the δ13C values were stable and similar in the littoral and deep zones, suggesting that littoral and deep chironomids relied on similar carbon sources; the HCs and cladoceran δ13C values were approximately −32‰, providing no evidence of organic carbon reworking via microbial mineralisation. From the 1930s to the 1950s, the littoral HC and cladoceran δ13C values decreased by 2‰. This decrease was probably related to an increase in respiration processes in the epilimnion following an increase in trophic state of the lake. The deep HC δ13C values remained stable during this period, suggesting that most of the additional primary production due to eutrophication was transferred to higher trophic levels. From the 1950s onward, the littoral HC and cladoceran δ13C values remained steady, whereas the deep HC values decreased substantially (−4‰), despite the restoration of oligotrophic conditions in open water. This pattern suggests the existence of organic carbon accumulation and microbial mineralisation at the lake bottom as well as a possible increase in methane-derived carbon consumption by chironomids. These processes were attributed to a lower trophic efficiency within the pelagic food web, decreasing the functional efficiency of the lake. Our results suggest that the functioning of the lake was characterised by low heterotrophic activities prior to the 1930s and that since the 1990s, the increase in heterotrophic activities has been supported by autochthonous organic carbon recycling.