Since the 1980s, high-nitrate concentration in one of the groundwater sampling wells at the Nankou site, northwest of the Beijing Plain, has become a major concern for the local water authority. In a previous study (Sun et al. in Environ Earth Sci 64(5):1323–1333, 2011), a hydrogeological structural model was developed based on the borehole logs of this area and the steady, as well as transient groundwater-flow models, were calibrated using the measured hydraulic heads. In this paper, the potential pollution sources in this area are investigated. The chemical analysis of the groundwater is also presented. The results demonstrate that the most likely pollution source is the untreated wastewater discharge from a nearby fertilizer factory. Furthermore, a mass transport model is developed to reproduce the nitrate transport process in the aquifer at the Nankou site under different pollution sources, i.e., a fertilizer factory, river with wastewater and an agriculture field. The combined effects of the river and agriculture fields present a better understanding of the nitrate transport in the local aquifer. In addition, a pumping scenario is designed to clean up the current nitrate concentration. The pumping rate and the well location are first estimated with 2-D analytical solutions of the type curves method. Then a 3-D numerical model is used to calculate the nitrate-concentration changes after the pumping activities start. In the downstream direction of the regional groundwater flow, three pumping wells are set up for the clean-up strategy. The calculated pumping rate in each well is about 1,500 m³/day. After 1 year, the nitrate concentration in the observation well recedes to 68 mg/l from the initial value of 72.9 mg/l, and it will be lower than the limitation value (20 mg/l) after 5,400 days of groundwater extraction. The data assessment and clean-up scenarios reported in this paper are fundamental for the contaminated aquifer management in the future.