Streams and ponds provide several ecosystem services but are threatened by anthropic activities. Studies on species contribution and local uniqueness are ways of analyzing sites that need conservation or restoration due to anthropic activities. These metrics are especially important when evaluating Amazonian environments, which are complex and understudied. In this study, we investigated the relationships between the local contribution (LCBD) and the species contribution (SCBD) to beta diversity and community attributes for zooplankton in Amazonian streams and ponds, and those between the land use change and local environmental factors on the LCBD (total, replacement, and richness difference). Additionally, we investigated whether sites with ecological uniqueness should be considered for conservation or restoration. We sampled zooplankton, macrophytes, and physical-chemical variables in 42 streams and 26 ponds in 2022. We also determined land use and land cover through digital image processing and calculated the Catchment Disturbance Index (CDI). A total of 130 taxa, comprising 76 rotifers, 41 cladocerans, and 13 copepods, were recorded. The zooplankton SCBD was positively correlated with species occurrence and abundance of individuals, while the LCBD was negatively related to abundance and species richness. In streams, total-LCBD was positively related to CDI and negatively related to macrophyte cover; in ponds, no significant relationship was observed. Our results improve current understanding of the effects of land use changes on zooplankton beta diversity, showing that more altered sites have unique and poor species composition and need restoration. Our data also increase knowledge on zooplankton in Amazonian environments, especially in streams that are understudied.