An increase in the spatial variability of rainfall is expected due to climate change. This implies increasing rainfall rates during spring and summer in the Pampas region, Argentina, period of maximum application of agrochemicals, which might cause an increase in pesticides and nutrients carried to surface water systems, as runoff by rainfall is one of the main pathways for diffuse pollution. The crops phenological stage can also affect pesticide and nutrient runoff since the applied agrochemicals and soil cover differ in each stage. In this study, we assessed the influence of rainfall and seasonal crop practices on water quality (nutrient and pesticide concentrations) in three streams in the Pampas region, Argentina. Five sampling campaigns were performed before and after three rainfall events during two different seasons of crop practices (SCP1, SCP2) and the physicochemical characteristics of the stream and runoff water were analyzed. The pesticide concentrations in the streams presented a general increase immediately after the rainfall event. Water quality was also affected, as an increase in ammonium, soluble reactive phosphorus (SRP), biological oxygen demand (BOD), and turbidity was observed. The crops phenological stage influenced pesticide and nutrient types and concentrations detected in the streams. During SCP1, mainly characterized by chemical fallow and sowing of soybean and vegetative growth and flowering of corn, ammonium, SRP, BOD, turbidity, and some pesticides, such as metolachlor, showed significantly higher results than those found in SCP2 (grain filling and vegetative growth of soybean and corn sowing). The pesticide concentrations detected in runoff water depended mostly on the pesticide solubility, the lateral slope of the streams, and the percentage of woody riparian vegetation cover. The results obtained show the relevance of assessing the influence of rainfall and crops phenological stages on the dynamics of surface water and on pesticide and nutrient runoff for environmental monitoring.