A 1100-year long record of lake ecosystem response to climate and catchment change with precise chronological control is reported. Diatom and pollen assemblages of an annually laminated (varved) sediment from a northern Swedish lake (Kassjon, Vasterbotten) were used as records of lake diatom communities and catchment vegetation. These data were compared with summer temperature estimates based on tree-ring records of the same geographical area to identify the effects of climate change and catchment disturbance on diatom assemblages in the lake. In a canonical ordination, 23% of the variability in the total diatom assemblages for the period AD1040-1804 was accounted for by changes in pollen data which reflect agricultural development in the catchment. Diatom species richness, however, exhibited a stronger relationship with summer temperature and, significantly, declined with the lower temperatures associated with the Little Ice Age minimum (early 17th century). Summer temperature accounted for 23% of the variability in diatom species richness 20 years later. The mechanism behind this time-lag is unclear, but may be related to catchment-mediated effects, given recent evidence for lags in the response of boreal-forest vegetation regeneration cycles to climatic variability. These results suggest that climate-related effects on lakes occurring over medium timescales can be resolved in lake sediments. Moreover, it is possible to identify these effects despite cultural-related signals, but as the latter become more extreme in the late 20th century the climate signal is obscured.