In New Zealand (NZ) 37% of monitored lakes are eutrophic, largely due to intensive agricultural land-use. Long-term lake ecosystem monitoring in NZ is rare and thus our understanding of how and at what point lakes transition from pristine to eutrophic states is limited. Diatoms are sensitive to changes in their environment, and are commonly used as indicators of lake trophic status and to reconstruct lake ecosystem response to anthropogenic impacts. Diatom cell size has also been shown to correlate with several environmental variables which represent ecosystem state, including nutrient concentrations, light and temperature. Thus, diatom cell size distributions may also be an indicator of lake ecosystem state. In this study, we assessed how the cell size distribution of diatom communities change in lakes with varying histories of agricultural land use, and whether cell size distributions indicate transitions to eutrophic states in lakes. We used paleolimnological records of six NZ lakes in varying degrees of agricultural impact to reconstruct diatom community composition and diatom cell size over the past 1000 years. Using regression tree approaches and ordination we analysed diatom cell size distributions for discontinuities over time. Preliminary results indicate that diatom cell size distributions exhibit marked shifts coinciding with changes in catchment land-use. These results suggest that diatom cell size distribution may be a useful indicator of ecosystem response to agricultural impacts. Further, measurements of diatom cell size may be a useful tool for the management of impending transitions in lake ecosystem state.