In recent years, climate events such as Drought, El Niño, and La Niña have become increasingly frequent and more intense. Oceanographic monitoring was used to collect hydrological data in the middle and lower sectors of the Caeté estuary in different years. Negative rainfall anomalies of up to 45% were recorded during periods marked by Drought and El Niño events, which make the water of the Caeté estuary more saline and alkaline. During these events, the retention of dissolved inorganic nutrients in the middle sector appear to support increased eutrophication and more productive waters, whereas moderate eutrophication and lower productivity were observed in the lower sector. During the La Niña events, by contrast, positive rainfall anomalies may reach 60%, resulting in more oxygenated water in the estuary. In addition, the lower sector tends to more eutrophic during periods of high rainfall and freshwater discharge, as observed in this study during a La Niña event. The paucity of data on the effects of extreme climate events in Amazonian environments means that the findings of the present study may provide a useful model for the assessment of the effects of these events on other natural environments in the Amazon region.