Using field and laboratory approaches, the water quality and biodiversity of plankton of in upper reaches, middle reaches, and lower reaches in the river taken as sources of water in scenic spots southwest of Yingde, China were investigated, with the aim to evaluate the spatial properties of hydro-ecological factors and the relationships between chemical parameters and plankton dynamics in different sections of the river. The concentations of phosphate, total phosphorus, nitrite, ammonia, nitrate, total inorganic nitrogen, and total nitrogen, heavy metals of aluminum, arsenic, cadmium, lead, copper, and zinc, and trace elements of calcium, cobalt, chromium, iron, magnesium, manganese, molybdenum, nickel, and selenium were measured, Population densities, species composition, and biodiversity index of phytoplankton and zooplankton were also examined. The levels of nitrite, ammonia, nitrate, total nitrogen, cadmium, lead, chromium, nickel, copper, and zinc in all sections of the river were within the environmental quality standard of surface water or sanitary standard for drinking water, but those of aluminum, calcium, cobalt, iron, molybdenum, and selenium in all sections of the river and those of total phosphorus, arsenic, magnesium, and manganese in some sections of the river exceeded the standards. Copepods were the dominant zooplankton in all sections of the river. The highest population density of zooplankton was in the section of Tongtianyan, the upper river reach, and the lowest biodiversity index of zooplankton was in the section of Biluohu, the lower river reach. 68 species of phytoplankton were found in the river, most of them inhabiting in the section of Biluohu. Population densities of chlorophyte, cyanophyte, and diatom were the lowest in the section of Biluodong, the middle river reach, those of chlorophyte and dinoflagellate were highest in the section of Tongtianyan, and those of cyanophyte and diatom were highest in the section of Biluohu. Along to the spatial trend from the upper reaches to the lower reaches, the concentrations of total phosphorus, total nitrogen, aluminum, and calcium and Shannon-Weaver biodiversity index of zooplankton increased, but the contents of manganese and nickel decreased. The relationships between chemical parameters and plankton were addressed. Results suggested that the water in the river studied should not be drunk directly, but it could be taken as the water in the landscape that should not be touched by people. This paper improved our understanding of the ecological structure and function of water-sources rivers in landscape, and can provide basic information for further managements of this ecosystem.