We examined the impact of lake trophic state on the taxonomic and functional structure of cladoceran communities and the role of nutrient loading in structuring both cladoceran and diatom communities. Surface sediment assemblages from 33 Irish lakes were analysed along a gradient of total phosphorus concentration (TP; 4.0–142.3 μg l−1), using a variety of statistical approaches including ordination, calibration and variance partitioning. Ordination showed that the taxonomic structure of the cladoceran community displayed the strongest response to changes in lake trophic state, among 17 measured environmental variables. Trophic state variables chlorophyll-a and TP explained about 20% of the variance in both cladoceran and diatom assemblages from a set of 31 lakes. Procrustes analysis also showed significant concordance in the structure of cladoceran and diatom communities (P < 0.001). Thus, lake trophic state affects the taxonomic structure of both primary and secondary producers in our study lakes. We also found a significant decrease in relative abundance of taxa associated with both macrophytes and sediments, or sediments only, along the TP gradient (r = −0.49, P = 0.006, n = 30), as well as an increase in the proportion of the planktonic group (r = 0.43, P = 0.017, n = 30). This suggests that cladoceran community structure may also be shaped by lake trophic state indirectly, by affecting habitat properties. We found no relationship between lake trophic state and the relative abundance of each of three cladoceran groups that display different body size. We compared community structure between bottom and top sediment samples in cores from six Irish lakes. Results revealed similar trajectories of nutrient enrichment over time, as well as a strong shift in cladoceran functional structure in most systems. This study confirms that Cladocera remains in lake sediments are reliable indicators of lake trophic state. This study also highlights the fact that taxonomic and functional structure should both be considered to account for the multiple factors that shape cladoceran communities.