The south-east margin of Tibet is highly sensitive to global environmental change pressures, in particular, high contemporary reactive nitrogen (Nr) deposition rates (ca. 40 kg ha−1 yr−1), but the extent and timescale of recent ecological change is not well prescribed. Multiproxy analyses (diatoms, pigments and geochemistry) of 210Pb-dated sediment cores from two alpine lakes in Sichuan were used to assess whether they have undergone ecological change comparable to those in Europe and North America over the last two centuries. The study lakes have contrasting catchment-to-lake ratios and vegetation cover: Shade Co has a relatively larger catchment and denser alpine shrub than Moon Lake. Both lakes exhibited unambiguous increasing production since the late 19th to early 20th. Principle component analysis was used to summarize the trends of diatom and pigment data after the little ice age (LIA). There was strong linear change in biological proxies at both lakes, which were not consistent with regional temperature, suggesting that climate is not the primary driver of ecological change. The multiproxy analysis indicated an indirect ecological response to Nr deposition at Shade Co mediated through catchment processes since ca. 1930, while ecological change at Moon Lake started earlier (ca. 1880) and was more directly related to Nr deposition (depleted δ15N). The only pronounced climate effect was evidenced by changes during the LIA when photoautotrophic groups shifted dramatically at Shade Co (a 4-fold increase in lutein concentration) and planktonic diatom abundance declined at both sites because of longer ice cover. The substantial increases in aquatic production over the last ca. 100 years required a substantial nutrient subsidy and the geochemical data point to a major role for Nr deposition although dust cannot be excluded. The study also highlights the importance of lake and catchment morphology for determining the response of alpine lakes to recent global environmental forcing.