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Zooplankton are regarded as a good indicator of environmental change, but comprehensive monitoring programs including zooplankton are uncommon and only rarely extend over longer periods of time. A part of the zooplankton community can be reconstructed using palaeolimnological methods, yet challenges remain. For example, cladoceran subfossil remains preserve selectively in sediments. In particular, the remains of Daphnia spp. are known to usually exhibit poor level of preservation; the reasons for this are still unclear. In the rural Lake Kivijärvi, located in central Finland, Daphnia subfossil remains preserve extraordinary well and multiple fossil components are found. However, the preservation level is not uniform and exhibits directional change throughout the sediment record. To investigate the changes in Daphnia preservation in lake sediments, we graded caudal spines from 20 fossil sediment samples into three taphonomic groups. A dataset of sediment geochemistry, diatom-inferred lake water pH, predation indices, and the catchment land use history was used to assess the environmental history of our study lake. In Lake Kivijärvi, the most significant change in Daphnia preservation seems to correspond best with the historical fishing activities. Additional explanatory variables include forestry in the catchment area, and pH, which, however, had contradicting effects on the preservation of Daphnia remains in this study. Finally, a fossil Daphnia longispina helmet type head shield derived from the lake sediment is presented for the first time.