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Summary1 Freshwater habitats in cultivated and densely populated lowland regions of Europe have experienced profound changes during the last 100 years. We take advantage of the long interest in aquatic plants in Denmark to compare the submerged¯ora in lakes and streams in 1896 and 1996. 2 Most of the lakes which contained a diverse submerged vegetation 100 years ago now have the high phytoplankton biomasses and summer transparencies below 2.0 m characteristic of eutrophication. The majority of 17 lakes included in both old and recent studies have lost all or most of their submerged species. Species richness for those lakes that were vegetated did not, however, dier signi®cantly between old and recent studies. 3 Species richness declined markedly in the 13 streams included in both studies. Over all sites, there was also a signi®cant decline of species richness per locality. Potamogeton species declined from 16 to 9, despite an 8-fold increase in the number of sites surveyed. 4 Similar compositions and rank-abundances of Potamogeton species in lakes and streams studied 100 years ago re¯ect suitable growth conditions and mutual exchange of propagules. Today, low habitat diversity and frequent disturbance in streams and low recruitment from lakes favours only robust, fast-growing species capable of regrowth following weed cutting and dredging. 5 A positive interspeci®c relationship observed in the contemporary stream vegetation between mean local abundance and number of occupied sites was probably promoted by redistribution of plants as a result of disturbance and ecient dispersal in the interconnected stream network. 6 The freshwater macrophyte¯ora in north-west Europe presently includes a high proportion of rare species which are threatened by extinction. Both species typical for oligotrophic conditions (e.g. P. ®liformis and P. polygonifolius) and another group of large, slow-growing species (e.g. P. alpinus, P. lucens, P. praelongus and P. zosterifolius), were once common but are now infrequent, while other transient species have remained rare (e.g. P. acutifolius, P. colouratus, P. densus and P. rutilus). The presence of many species that barely survive in small and distant populations will make re-assembly of submerged aquatic communities dicult.

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.

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