Central China, one of the Earth’s distinctive ecoregions due to its endemic subtropical biota, has been subjected to enhanced nitrogen deposition and climate warming during recent decades. However, the extent and timescale of ecological changes are largely unexplored. Multiproxy analyses (diatoms, photosynthetic pigments and geochemistry) of 210Pb-dated sediment cores from two shallow ponds within an alpine basin (central China) were used to investigate the response of primary producer communities to external stressors during the last two centuries. The study sites include one drainage pond and one seepage pond. Both ponds exhibited unambiguous changes in production and composition of photoautotrophs since the early twentieth century, which are linked to climate warming, nitrogen deposition and local factors (for example, lake morphometry, desiccation and macrophyte). Although primary producers responded to regional warming and nitrogen deposition, the ecological responses differed among ponds due to local factors. In the deeper seepage pond, light attenuation due to terrestrial organic matter input caused recent decreases in carotenoids and small fragilarioid taxa. In contrast, the co-occurrence of euterrestrial and tychoplanktonic diatoms in the shallower drainage pond was indicative of its hydrological instability. Our results indicate that subtropical montane ponds in the East Asian monsoon region appear to be strongly influenced by a combination of local (for example, catchment-lake connectivity) and regional driving forces (for example, warming and nitrogen deposition).