Freshwater species are facing massive declines, often driven by eutrophication. Identifying which facets of biodiversity are sensitive is crucial, as species loss does not always translate to reduced ecosystem functioning and functional diversity. We examined how assembly rules shape zooplankton functional diversity in hypereutrophic fishponds. Higher eutrophication was hypothesized to cause functional homogenization through reduced functional diversity, habitat filtering, and trait convergence. Higher eutrophication indeed reduced functional diversity metrics, while species richness was kept stable. Functional richness, dispersion, and dissimilarity shifted from limiting similarity, where niche partitioning and competition shape community structure, to random (incidence data) and habitat filtering (biomass) with increasing eutrophication. Functional divergence transitioned from random to habitat filtering, while redundancy increased at higher trophic states. Trait convergence was the dominant process, with the environment selecting species with similar traits. Biodiversity assessments and managers should consider how functional diversity and ecosystem functions respond to anthropogenic and environmental changes.