As cladocerans are a primary food source for fish, predator avoidance is important to sustain cladoceran populations. We hypothesized that Bosmina longirostris and Daphniaobtusa would show different vertical distributions that depend on environmental variables and their life cycle phase. Quarterly monitoring was implemented in three water column layers (upper, middle, and bottom) in the Nakdong River Estuary. Cladocerans were mostly observed during summer; B. longirostris and D.obtusa were most abundant and exhibited different vertical distributions. Large (>600 μm) D.obtusa individuals were mainly distributed in the bottom layer (9–11 m) during the daytime and in the upper layer (1–3 m) at night. Utilization of the bottom layer by large D. obtusa was possibly a defense strategy to avoid fish predation. Although the bottom layer was not supported by lower water temperatures and dissolved oxygen than the upper or middle layers, as suggested in the previous study, we assumed that high turbidity replaced this role as a place shunned by fish (and thus a refuge for Daphnia obtusa). In contrast, smaller individuals remained in the upper layer at all times because of the low predation risk. The consumption of B. longirostris by fish was low, as the largest B. longirostris (411 μm) was smaller than the small-sized Daphnia. From this finding, we suggest that the vertical distribution of cladocerans likely depends on selectivity feeding based on fish size rather than the presence/absence of fish. We considered that these results are an important advance in understanding distribution patterns of cladocerans related to environmental features, as well as their key predators.