Eucalyptus can grow into wood in two or three years and has large-scale cultivation in the southern China, with high economic value. Recently it is considered "pump", "green desert", and even rumoured "toxic." The water in the reservoir in Eucalyptus planting area appeared "black" sporadically. The water was dark brown with a pungent smell, which has caused great panic within local residents. The phenomenon is associated to Eucalyptus trees plantation. To explore the mechanism of "blackwater" in the reservoir in Eucalyptus plantation, southern China, three typical reservoirs (Najiang, Tianbao, Baihe Reservoirs) were selected in Eucalyptus planting area. Main water quality variables including hydrological and environmental factors were observed 4 times, from August 2015 to April 2016. The physicochemical indexes of water were determined, and then synthetic analysis was performed combined with hydrological data provided by the Nanning Metrological Station. The results indicate that reservoirs in Eucalyptus forest area blackening are associated with a particular season and special climatic conditions. Meanwhile, the instability of water temperature stratification structure is the main driving factor of black materials transport. In summer, hierarchical structure, the water temperature in reservoirs keeping thermal stratification structure stable, results in dissolved oxygen and other water quality indexes were changing with stratification and limits transporting upward. In autumn and winter, stratification disappears, and vertical exchange of water body provides the underlying pollutants with upward force. Finally, pollutants spread the whole body and lead "blackwater" phenomenon. Seasonality and spatial heterogeneity of sulfide, tannic acid, iron, manganese and other materials is closely related to the seasonal characteristics of water temperature stratification. In the Eucalyptus forest reservoirs, iron and manganese concentrations are up to 2.93 and 3.46 mg/L, respectively. A large amount of tannic acid appeared when Eucalyptus leaves soaked in the water. When sulfide, tannic acid, iron and manganese exist together, a series of reactions such as iron, manganese and sulphur, sulphur and tannic acid, iron, manganese and tannic acid can produce black complex. Our results can provide guidance in guaranteeing the safety of drinking water sources in Eucalyptus planting area and lay the foundation for the further research of black water.