Shallow lakes have been affected by a variety of human activities profoundly altering their ecological structure and function. Cladocerans have been used to track change resulting from a variety of drivers at a number of time scales. Aquatic macrophytes are well recognised as reflecting the ecological condition of a lake. Here, we compare the plant macrofossils with the sub-fossil cladoceran assemblages from 20 dated sediment cores. Co-correspondence analysis was used to determine the degree of commonality of change in community composition of the two biological groups through time. This analysis revealed very high levels of agreement in the nature and timing of change at all the sites examined with very high correlation coefficients between the axis 1 scores for macrofossils and cladocerans. Furthermore, at all sites a high proportion of the variance (min 20%, max 54%) in the macrofossil data was explained by the change in the cladoceran assemblage. Sub-fossil macrofossil and cladoceran assemblages, from at least from 1700 AD onwards, were examined in more detail at three sites: Ormesby Great Broad, Felbrigg Lake and Lake Søbygaard. There was very good accord in the main shifts of the cladoceran and macrofossil assemblages at all three sites. This may reflect the long-term shift in the principal focus of primary production from the benthic to the pelagic habitat. We suggest that the combination of their central position in the food-web and the presence of both pelagic and benthic taxa make cladocerans a strong candidate as the single best indicator of (palaeo) ecological condition related to changing trophic status and alteration in food-web structure in shallow lakes.