During the past few decades, the majority of shallow lakes in the Yangtze River basin (Eastern China) have been impacted by heavy discharges of sewage and the intensification of aquaculture. These activities have significant potential to alter aquatic ecosystems and these changes may be reflected in the composition of lipid biomarkers in sediments at the time. In order to evaluate this effect, the abundances and distribution of fatty acids (FAs) were measured in ²¹⁰Pb dated sediment cores from two anthropogenically impacted shallow lakes in the Yangtze River basin, Changdang and Taibai. Results from Lake Changdang revealed an extreme enrichment of zooplankton-derived C22:1 ω11 in sediments, with C22:1 ω11/n-C16 ratios reaching ~1.6 on average. This unusual distribution may have been caused by zooplankton blooms in the lake in the years before aquaculture was developed. Elevated abundances of C18:1 ω9 and short-chain n-alkanoic acids observed in pre-1977 sediments might be also derived from zooplankton. After 1977, FAs of zooplankton origin in Lake Changdang greatly declined in abundance, coincident with the introduction of planktivorous fish. Meanwhile, inputs of FAs from submerged/floating macrophytes, bacteria and algae increased as a result of eutrophication and reduced grazing pressure from zooplankton. In Lake Taibai, abundances of C22:1 ω11 were greatly reduced in all sediments and accounted for 38% of n-C16 on average, reflecting comparatively smaller inputs of zooplankton FAs owing to the earlier establishment of aquaculture in the lake. Relative enrichment of polyunsaturated FAs (PUFAs) and branched FAs (Br-FAs) in the sediments was attributed to high inputs of algal and bacterial organic matter (OM) in response to reduced predation and grazing by zooplankton. Rapid increases in PUFAs and Br-FAs in post-1970 sediments were driven by eutrophication in this period.