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Plankton communities constitute an important part of the biodiversity in shallow lentic ecosystems (SLEs). Understanding their diversity responses to increasing human pressure is required for the effective management of SLEs. Here we assessed the relationship between different properties of phytoplankton and zooplankton communities (abundance, taxonomic and functional diversity, and taxonomic and functional composition) and human impact (HII index), limnological features of SLEs (i.e., surface area and depth, trophic state, and hydrological connectivity), the biomass of submerged macrophytes, and the abundance of planktivorous fishes. For this, we sampled zooplankton from 28 sampling sites across nine SLEs (seven ponds, one channel, and one shallow lake). For 18 sampling sites across six of the ponds, we also sampled phytoplankton. We found that phytoplankton abundance was negatively associated with the higher HII, while zooplankton abundance and species richness increased with increasing HII. Hydrological connectivity was an important predictor of both phytoplankton and zooplankton diversity and composition. The functional diversity and composition of phytoplankton were more sensitive to environmental changes than their taxonomic diversity. Opposite patterns were recorded for zooplankton diversity metrics, presumably due to the dominance of non-predatory rotifers, which maintained constant functional diversity despite variations in taxonomic diversity along environmental gradients. Our results suggest that the taxonomic and functional diversity metrics of both phytoplankton and zooplankton should be considered simultaneously since they can show contrasting responses to human pressure and environmental changes in SLEs. © 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.