The cladoceran fauna is well studied across the Palaearctic, but remains poorly known in the Republic of Tyva, Russia. Our database represents the results of the faunistic survey of the cladocerans in this region performed during almost 30 years (1993–2022). A total of 902 sites were investigated, most of them being located in mountain areas (49°45' – 53°46' North latitude and 88°49' – 98°56' East longitude). The dataset includes the cladocerans sampled from permanent and temporary waterbodies with varying depths, altitudes and salinity levels. Sampling was conducted using plankton nets and then samples were transported to the Tuvinian Institute for Exploration of Natural Resources of the Siberian Branch of RAS for identification and further examined at the A.N. Severtsov Institute of Ecology and Ecology RAS. Species were identified, based on recent monographs and juvenile specimens (sometimes indeterminable, based on morphological methods) were excluded from the dataset. The dataset was published as a Darwin Core Archive in GBIF. For each sampling event, the coordinates of the location, date and collector are recorded. The dataset contains information on zooplankton and microzoobenthos from numerous permanent and temporary waterbodies in the Republic of Tyva, Russian Federation. Previously, the region’s cladoceran fauna was poorly studied. Our core data table includes 3,599 records representing 76 species from 902 locations. The most species-rich families are Chydoridae (30 species from 17 genera) and Daphniidae (26 species from 5 genera). No invasive species were detected. The results of this study contribute to a deeper understanding of the plankton and microzoobenthos communities in the Central Asian mountain regions.