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Insight into the causes and consequences of changes in aquatic biodiversity requires an improved understanding of the nature of the relationships between species richness and ecosystem function over a much longer temporal perspective than we currently possess. We used high-resolution paleoecological records from two prairie lakes to show that diatom species richness (as fossil frustules) was negatively correlated (r² = 0.09-0.24, p < 0.001) with diatom production (as fossil pigments) during the past 2,000 yr. By comparing analyses from intervals of fresh and saline waters, we demonstrate that these significant richness-production relationships arose during freshwater periods (r² = 0.13-0.45, p < 0.001) and could be eliminated (r² < 0.02, p > 0.1) by abiotic disturbances such as droughts. Procrustes analyses of the concordance of species change within freshwater communities and the change in richness--production relationships through time revealed that shifts in diatom community composition could have a large influence in determining the negative relationship between richness and production. Finally, significant correlations (r² = 0.09-0.24, p < 0.0001) between past diatom species richness and ratios of stable isotopes (primarily δ15N) suggested that C and N biogeochemical cycles are also linked to changes in algal biodiversity. Taken together, these analyses suggest that the ongoing disruption of climate and biogeochemical systems by humans may obscure the relationship between aquatic biodiversity and ecosystem function in the future. [ABSTRACT FROM AUTHOR]