1. A sediment core from the shallow, hypertrophic Lake Søbygaard (mean depth ∼1 m; [TP] 310 μg P L−1) was analysed for subfossil remains to reconstruct chironomid community changes in relation to the succession and disappearance of aquatic macrophytes.
2. Species composition in the 1.10 m core indicates a succession from a ‘naturally’ eutrophic state to a hypertrophic state during recent centuries. Radiometric dating (210Pb) of the uppermost 20 cm of the sediment core (∼1932–93) indicates that sediment accumulation rate had doubled in recent decades.
3. Changes in chironomid assemblages were in close agreement with changes in both diatoms and macrophyte remains in the same core. Distinct changes in chironomid communities reflect the eutrophication process and macrophyte succession through Chara, Ceratophyllum and Potamogeton dominance to the present state, with complete loss of submerged vegetation and dominance by phytoplankton.
4. The co-occurrence and relationship between aquatic macrophyte diversity and recent subfossil chironomid assemblages were assessed from an additional 25 Danish lakes. There was good agreement between the macrophyte and chironomid-based lake groupings. Overall, a significant difference (P<0.001) was found in chironomid assemblages among lakes in different macrophyte classes. In a pair-wise comparison, the poorly buffered mesotrophic lakes and the alkaline eutrophic lakes had significantly different chironomid assemblages.
5. Chironomid taxa commonly reported to be associated with macrophytes (Cricotopus, Endochironomus and Glyptotendipes) were shown also to be indicators of highly productive lakes lacking abundant submerged vegetation.