Abstract: Well water is the main source of drinking water in subtropical agricultural regions in China, and its quality is critical for human health. In this paper, we carried out a geostatistical analysis to investigate the seasonal changes and spatial variability in the concentrations of ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), total nitrogen (TN) and total phosphorus (TP) in domestic well water in a typical agricultural catchment in southern China. Our results showed that the average concentrations of NH₄⁺-N, NO₃^--N, TN and TP in spring, summer, autumn and winter of 2013–2014 were in the ranges of 0.050.10 mg(N)·L^-1, 3.04.9 mg(N)·L^-1, 3.45.1 mg(N)·L^-1 and 0.030.17 mg(P)·L^-1, respectively. The observed concentrations of NH₄⁺-N, NO₃^--N, TN and TP exceeded the national standards in terms of frequency by 2.3%, 10.4%, 9.5% and 7.9%, respectively. Temporally, NO₃^--N, TN and TP were significantly (P < 0.05) higher in summer and lower in spring, mainly resulting from paddy rice fertilization and precipitation. On the contrary, there was no significant difference in seasonal concentrations for NH₄⁺-N, mainly due to soil retention. In terms of spatial variability, these four variables were strongly auto-correlated in space and with different spatial ranges for different seasons. In terms of spatial distribution, the high NH₄⁺-N, NO₃^--N, TN and TP concentrations were distributed as patches, even though their locations, sizes and shapes varied from one another. The concentrations of NO₃^--N and TN were high in the southeast and southwest of the catchment, where rice was cultivated in the low topography. But the concentrations of NO₃^--N and TN were low in the north, where there was forest plantation on the high topography. This result suggested that the spatial distribution of NO₃^--N and TN in well water were related to topography and land use type in the catchment. The spatial coefficients of variation of NH₄⁺-N and TP were higher than those of NO₃^--N and TN. This was mainly attributed to the strong adsorption and immobilization of NH₄⁺-N and phosphate in the soil matrix, resulting in the differences in NH₄⁺-N and TP concentrations at different locations. The main factors affecting the seasonal change and spatial variability of well water quality in subtropical agriculture region were topography, regional hydrological and climatic conditions, soil types, land use types and agricultural fertilization.