Water quality in the Banchengzi reservoir in Beijing has been deteriorating year by year, and it was embodied by increasing concentrations of COD and stable but high levels of total nitrogen. In order to identify the causes and to formulate a strategy for pollution prevention and control, we examined the temporal and spatial variations of water pollution and carried out source identification studies. Routine monthly monitoring data for seven water quality and six hydro-meteorological variables of the Banchengzi reservoir from 2007 to 2012 were analyzed by statistical techniques, including correlation analysis and principle component analysis. In addition, water samples at six different sites in the reservoir were collected and analyzed to investigate the spatial variation of water quality and to further identify the water pollution sources by UV-vis spectroscopy, three-dimensional excitation-emission matrix spectroscopy, and nitrogen stable isotope (N-15) analysis. The results revealed that dissolved organic matter and nitrogen were the main pollutants and were principally derived from anthropogenic point source pollution in the upper areas, which included domestic sewage and livestock farming. We speculated that the biodegradable organic pollutants from sewage were degraded to form soluble microbial products (SMP) by aerobic microorganisms and that nitrogen pollutants were mostly transformed to nitrate by nitrification. These SMP, nitrate, and other refractory pollutants were carried by the upper stream flowing into the Banchengzi reservoir, where it accumulated. Effective control of point source pollution and upper river ecological restoration should be done to improve the water quality and protect the reservoir.