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The zooplankton community in a relatively small and mountain pond was studied during the spring growing season. To investigate which factors operate in the community structure, we explored several physical conditions, such as high inflows, and the biotic dynamics of the main zooplankton groups (i.e., rotifers, cladocerans and copepods). Two extreme flood events occurred during the investigated period and caused dramatic changes in physical conditions and reduction of the planktonic community abundances. The short period between both high-flow events was enough for the recovery of microplankton, but not for the metazoan zooplankton. Our results are in agreement with the common situation in which high flood events commonly favour rotifers over crustaceans, likely due to rotifer species have great colonization ability and grow faster. However, we found that the dominance of rotifers over crustaceans in our system is evidenced by an extremely, unusual high ratio between their abundances. We observed that, at the time of the great floods, crustacean abundances as well as rotifer populations notably decreased until near zero values. Although rotifer abundance began declining before high floods, the decrease was particularly notable when the great flood happened. Our results evidenced that i) dilution rate and temperature were the main drivers which are operating in the structure of the zooplankton community; and ii) no negative biotic interactions were detected between large and small cladocerans and rotifers. Additionally, we found surprisingly that a repeated disturbance caused by high flood events does increase the species diversity of rotifers. Finally, our study also detected some cues which may indicate that diapausing egg bank is also playing an important role in the zooplankton community, favouring the dominance of rotifers; however, this phenomenon deserves further studies.