Rainfall and runoff characteristics may influence off-site export of pesticides into downstream aquatic ecosystems. However, the relationship between rainfall characteristics and pesticide export from small headwater catchments remains elusive due to confounding factors including the application dose and timing and the variation of pesticide stocks in soil. Here we examined the impact of rainfall characteristics on the export of copper (Cu), zinc (Zn) and 12 legacy and currently used synthetic pesticides in surface runoff from a headwater vineyard catchment. Cluster analysis of rainfall intensity, depth and duration of 78 events revealed four distinct rainfall categories, i.e., Small, Long, Moderate and Intense (p < 0.001). Event mean concentrations of pesticides did not differ among rainfall categories (p > 0.05). In contrast, event loads of both dissolved and solid-bound Cu and Zn significantly differed among rainfall categories (p < 0.001). Rainfall depth and intensity significantly correlated with both Cu and Zn loads in runoff (ρs = 0.33 to 0.92, p < 0.002), and might be the main drivers of Cu and Zn export at the catchment scale. In contrast, rainfall depth, intensity or duration did not influence the loads of synthetic pesticides in runoff, even when weekly variations of pesticide stocks in the soil were accounted for. However, intense rainfall-runoff events, that can fragment soil, may control the export of persistent and hydrophobic legacy pesticides stocks in the soil, such as simazine and tetraconazole. Our results show that rainfall characteristics controlled the off-site export of Cu, Zn and legacy synthetic pesticides in a small headwater catchment, whereas the application timing drove the export of currently used synthetic pesticides in runoff. We anticipate our results to be a preliminary step to forecast the influence of regional rainfall patterns on the export of both metallic and synthetic pesticides by surface runoff from small agricultural headwater catchments.