Summary1. Changes in nutrients and climate have occurred over approximately the same timescales in many European lake catchments. Here, we attempt to interpret the sedimentary diatom record of a large shallow lake, Loch Leven, in relation to these pressures using information gained from analysis of long‐term data sets of water quality, climate and planktonic diatoms.2. The core data indicate the enrichment of Loch Leven starting in c. 1800–1850, most likely from agricultural practices in the catchment, with a more marked phase since c. 1940–1950 caused by increased phosphorus inputs from sewage treatment works, land drainage and a woollen mill.3. While the recent diatom plankton remains are dominated by taxa associated with nutrient‐rich conditions, an increase in Aulacoseira subarctica relative to Stephanodiscus taxa since the mid‐1980s suggests that reductions in external catchment sources of nutrients (since 1985) may have resulted in partial recovery. This observation accords well with the long‐term monitoring series of water chemistry and phytoplankton.4. On a decadal‐centennial scale, the eutrophication signal in the sediment record outweighs any evidence of climate as a control on the diatom community. However, at an inter‐annual scale, while the diatom data exhibit high variability, there are several changes in species composition in the recent fossil record that may be attributed to climatic controls.5. The study highlights the value of a palaeolimnological approach, particularly when coupled with long‐term data sets, for developing our understanding of environmental change at a range of temporal scales. The diatom record in the sediment can be used effectively to track recovery from eutrophication, but requires greater understanding of contemporary ecology to fully interpret climate impacts.6. The study illustrates the complexity of ecosystem response to synchronous changes in nutrients and climate, and the difficulty of disentangling the effects of these multiple, interacting pressures.