Summary Multi‐indicator palaeoecological studies have become increasingly popular over the last decade as the need for a more complete understanding of lake ecological histories has increased. However, the true potential of the full biological record for assessing the potential drivers of observed ecological shifts in lake sediment records has rarely been demonstrated. Here, we examine the remains of a range of food‐web components including algae (diatoms), macrophytes (plant macrofossils), zooplankton (chitinous and ephippial Cladocera remains), invertebrates (including chironomids, bryozoans, Mollusca) and fish (fish scales and fish leech egg cocoons) in multiple sediment cores from Groby Pool, an enriched English shallow lake, to assess whole‐ecosystem response to eutrophication over the last two centuries. We focus on three striking changes in the palaeorecord, namely the post‐1900 increase in Daphnia spp., the post‐1840 decline in Cristatella mucedo and the post‐1940 increase in Cocconeis placentula, and utilise the multi‐indicator palaeoecological data to evaluate possible explanations for these patterns. Principal curves analysis revealed marked and broadly simultaneous changes in the plant macrofossils, cladocerans, diatoms and chironomids (as well as in other animal remains such as bryozoans and Mollusca), indicating an early period of enrichment most likely associated with land‐use change in the late 18th century, followed by a more recent eutrophication phase coincident with the discharge of sewage effluent to the lake from 1935. Ecological change, resulting from eutrophication, was shown to have progressed slowly and steadily and to have occurred at all trophic levels with a shift from a relatively diverse ‘mesotrophic’ macrophyte assemblage, dominance by benthic diatoms and plant‐associated Chydoridae and chironomids towards a relatively species‐poor, ‘eutrophic’ macrophyte community with dominance by planktonic algae (e.g. Cyclostephanoid diatom taxa), planktonic Cladocera (Bosmina, Daphnia) and a chironomid fauna dominated by mud‐associated taxa. The inferred shift in the macrophyte community from charophyte to fine‐leaved pondweed and Callitriche truncata suggests a reduction in the seasonal duration of plant dominance. The multi‐indicator analysis indicates that a combination of increased phytoplankton biomass and low zooplanktivorous fish predation is likely to explain the recent increases in Daphnia spp., while loss of plant habitat and increased competition for food appear to be the most likely causes of the observed decline in C. mucedo, and resistance to increased grazing pressure from invertebrates is the most probable driver of the C. placentula increase. Our study illustrates the potential of using the full array of fossil groups preserved in lake sediment cores to infer ecosystem dynamics over centennial timescales and to contribute to our understanding of the mechanisms that may link biological assemblages to a range of forcing factors. Further, this paper provides methodological guidance by demonstrating the ability of amalgamated records from three cores to reveal a strong sequence of events and coherent patterns.