Climate change is predicted to influence the heat budget of aquatic ecosystems and, in turn, affect the stability of the water column leading to increased turbulence coupled with enhanced turbidity. However, the synergetic effects of turbulence and turbidity on zooplankton community structure remain to be understood in large, shallow lakes. To determine the possible synergetic effects of these factors on zooplankton communities, a 15-day mesocosm experiment was carried out and tested under four turbulence and turbidity regimes namely control (ɛ = 0, 7.6 ± 4.2 NTU), low (ɛ = 6.01 × 10-8 m2 s-3, 19.4 ± 8.6 NTU), medium (ɛ = 2.95 × 10-5 m2 s-3, 55.2 ± 14.4 NTU), and high (ɛ = 2.39 × 10-4 m2 s-3, 741.6 ± 105.2 NTU) conditions, which were comparable to the natural conditions in Lake Taihu. Results clearly showed the negative effects of turbulence and turbidity on zooplankton survival, which also differed among taxa. Specifically, increased turbulence and turbidity levels influenced the competition among zooplankton species, which resulted to the shift from being large body crustacean-dominated (copepods and cladocerans) to rotifer-dominated community after 3 days. The shift could be associated with the decrease in vulnerability of crustaceans in such environments. Our findings suggested that changes in the level of both turbidity and turbulence in natural aquatic systems would have significant repercussions on the zooplankton communities, which could contribute to the better understanding of community and food web dynamics in lake ecosystems exposed to natural mixing/disturbances.