We investigated the diel vertical distribution patterns of microcrustacean zooplankton (Cladocera, Copepoda) in a shallow pond (max. depth: 70 cm) of the Öreg-turján peatland (Ócsa, Central Hungary) during three 24-h periods in July (19–20th), August (17–18th) and September (11–12th) 2011. Environmental variables showed remarkable vertical stratification. Oxygen concentration was close to zero in the entire water column from night until sunrise, while the lower strata (from 20 cm below the surface) were close to anoxic during all three diel cycles. It proved to be the main determinant of the vertical distribution of microcrustaceans. Accordingly, the highest proportion of individuals was present in the surface layer. Chlorophyll-a concentration and phytoplankton biomass were inversely distributed compared to zooplankton. Microcrustaceans (mainly Daphnia curvirostris) migrated to the middle layer only in August, which could be explained by a trade-off between food resources, dissolved oxygen (DO) and competition with littoral zooplankters. The diurnal density patterns of microcrustaceans suggested horizontal migration into the aquatic macrophytes during night, which could be a strategy to avoid Chaoborus predation. Our results show that strong vertical gradients of abiotic and biotic factors occur even in such shallow waterbodies. Among them, DO can maintain constant vertical aggregation of zooplankters by limiting their occurrence to the surface layers.