How the environment impacts the assembly of local communities as well as their spatial and temporal connection in a metacommunity has remained a largely unresolved question in community ecology. This study aims to unravel the underlying metacommunity dynamics and environmental factors that result in observed zooplankton communities. In extension to most studies concerning metacommunity dynamics, we jointly examine zooplankton communities both in open water and in the sediment where zooplankton resting stages/dormant communities are stored. We used a two-fragment DNA metabarcoding approach (COI and 18S) to monitor zooplankton communities of 24 kettle holes over a two-year period to unravel (I) how the community is spatially and temporally connected, (II) what are the environmental factors influencing local communities, and (III) what are the underlying metacommunity dynamics in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (ephemeral vs. permanent) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and hydroperiod, while species diversity was influenced by kettle hole location. Community composition was further impacted by kettle hole size, water temperature and pH. Soil samples showed a separate community composition compared to water samples, but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, water temperature, kettle hole size and hydroperiod. Species sorting is a dominant driver in community assembly in the studied kettle hole zooplankton metacommunity.