Given the unprecedented and growing threats to inland waters — eutrophication, cyanobacterial blooms, over-exploitation, and climate change — from multiple human activities, biodiversity is decreasing at faster rates in freshwater ecosystems than in marine or terrestrial. Since the early 1990s, hundreds of studies attempted to explain how ecosystems respond to biodiversity loss and how changes in biodiversity scale up to affect ecosystem functioning, as well as the provision of goods and services to humans. Recent studies have demonstrated that such biodiversity responses are commonly trait-mediated and the effects of communities on ecosystem functioning also depend on species traits. However, it remains unclear to what extent such biodiversity responses translate into changes in the rates of many ecosystem processes in naturally assembled communities. In this doctoral dissertation, I aimed at evaluating the effects of nutrient availability and cyanobacteria dominance on structure and composition of plankton communities (phytoplankton and zooplankton), and on two important ecosystem functions in aquatic systems: phytoplankton resource use efficiency (RUE) of limiting nutrients — phosphorus and nitrogen — and zooplankton top-down control of algae. For this, I structured this doctoral dissertation in three chapters to explore the mechanisms that underlie biodiversity-ecosystem functioning (B-EF) relationships, using a combination of experimental and fieldwork approaches, together with multiple aspects of biodiversity (i.e., taxonomic and functional diversity). In the first chapter, I and my coauthors analyzed the relationship between different measures of phytoplankton diversity, temporal turnover and RUE using 8-years monitoring data set from a cyanobacteria-dominated subtropical lake, which is now experiencing a shift in the trophic state from oligo-mesotrophic to eutrophic. Additionally, we aimed at evaluating the effect of resource availability on phytoplankton community structure and RUE. In the second chapter, using 1-year monitoring data set from the same lake, we evaluated the relative importance of size-based and taxon-based approaches in explaining the strength of zooplankton top-down control on algae, and also aimed at disentangling the mechanism by which zooplankton body size drives such ecosystem function. Finally, in the third chapter, we used an experimental metacommunity approach that simulated typical gradients of productivity and plant structural complexity to test how zooplankton body size diversity and composition responded to such gradients and whether and how such trait responses impacted top-down control of algae. Through these three chapters, we demonstrated that under environmental changes (i.e., nutrient increase and prolonged cyanobacteria dominance) approaches based on body size and taxonomic richness complement each other in explaining variation in zooplankton top-down control. Our results clearly indicate that zooplankton body size explains a substantial and independent part of the variance in top-down control, which corroborates several studies demonstrating the role of zooplankton body size to control phytoplankton biomass. But contrary to our expectations, species richness also plays a role, indicating that species richness may adequately represent some unmeasured traits that also influence ecosystem functioning. Moreover, we demonstrated that different aspect of biodiversity might have divergent responses and divergent effects on ecosystem functioning depending on environmental perturbation, which highlight the importance of considering multiple aspects of biodiversity — taxonomic and functional approaches — in B-EF research. Overall, our results illustrated the potential for trait-based approaches to reveal biodiversity responses to environmental change and their generalizable effects on ecosystems. Furthermore, given the lack of large grazers in tropical and subtropical regions, and the evidence that Cyanobacteria dominance will increase in freshwater ecosystems under the predicted future climate, the results herein highlight the concern about the energy flow in aquatic systems dominated by Cyanobacteria.