This study sought to determine the potential of sedimentary cladoceran assemblages for inferring changes in shallow lake ecological structure and function. The first stage of the study aimed to isolate and quantify the main structuring forces of the contemporary zooplankton community. Zooplankton populations were sampled from 39 mesotrophic to hyper-eutrophic shallow lakes (<3 m average depth) in the U.K. and Denmark. Additionally, a suite of environmental variables, including: fish, macrophytes, algal crop, nutrient concentrations and water transparency were analysed. A variety of numerical techniques including constrained ordination and logistic regression were employed to determine whole community and individual species response to the environmental variation within the data set. The sedimentary remains of zooplankton were then enumerated from the surface sediments of the 39 'training set' lakes. These data were compared with the contemporary counts. Despite differential preservation of sedimentary remains, the main factors structuring the assemblages were the same in both data sets, zooplanktivorous fish density (ZF) and submerged macrophyte abundance (MA). Furthermore, these factors displayed a similar degree of influence on both assemblages. A multivariate regression tree (MRT) was used to calibrate sedimentary cladoceran assemblage response to ZF and MA. The resultant model places a site in one of five groups based on cladoceran assemblage and corresponding to a range of values of ZF and MA. These groups represent distinct forms of ecosystem structure and function varying from sites with clear water, abundant macrophytes and low ZF to turbid, phytoplankton dominated systems with high ZF. Sedimentary cladoceran assemblages from dated cores for two sites, Felbrigg Lake (Norfolk, England) and Kenfig Pool (Glamorgan, Wales) were analysed. The cladoceran inferred ZF and MA indicated that both sites have undergone dramatic changes in ZF and MA. Comparison with plant macrofossil data and historical records at both sites indicated the veracity of the model