Extreme climatic events are considered one of the main consequences of climate change. In the Pampas region, Argentina, an intensification of rainfall is expected during the periods of maximum agrochemical application. This study assesses the main factors determining the zooplankton community attributes in three streams belonging to the agricultural Pampas region, Argentina, and the effect of rainfall and seasonal crop practices on the zooplankton community composition. Sampling campaigns were performed before and after three rainfall events during two seasonal crop practices: (1) soybean chemical fallow-sowing and corn vegetative growth-flowering, (2) soybean vegetative growth-grain filling and corn sowing. The runoff in agricultural areas affected the zooplankton community attributes and composition. The biological oxygen demand, turbidity, and conductivity were the main water quality variables affecting the zooplankton community attributes. The increase of these variables after rainfall or during pre-emergence crop practices favoured the zooplankton groups most tolerant to eutrophication such as Bdelloidea, Chydoridae, Moinidae, and Sididae. Factors such as rainfall and seasonal crop practices must be considered in environmental monitoring design.