Theory predicts that ecosystems under stress change in their structure and functioning and these alterations may be symptomatic of potential breakdown in overall ecosystem functioning due to homeostatic regulation. In this dissertation, I present four studies looking at how ecosystem functioning in thirty-two freshwater lakes changes as a result of stress from anthropogenic eutrophication using paleolimnological and contemporary sampling techniques. In particular these studies looks at the changes to algae (diatom) community structure and production, organic carbon (OC) cycling, importance of external inputs of eroded sediment and nutrients, and resource use efficiency (RUE) of zooplankton. I found significant changes in both structure and production of the diatom community and a predictive model for phosphorus enrichment using diatom community assemblages. I found significant increases in OC burial correlated with nutrient enrichment and the intensification of agriculture. I also found increasing rates of erosional deposition from the watershed to these lakes as well as nutrient-stimulated in-lake production. In my final study, I found a decrease in RUE of zooplankton in eutrophic systems which was greater than previously predicted. This decline in RUE was likely correlated to increases in Cyanobacteria biomass, following anthropogenic eutrophication, which are larger and more difficult for zooplankton to consume. Together, these four empirical studies suggest that as anthropogenic eutrophication continues to become more prevalent, the ecosystem functioning of freshwater lakes worldwide will be significantly altered.