The objectives of this study were to investigate the effects of rainfall and underlying surface conditions on nonpoint source (NPS) pollution loads and to identify the uncertainty in NPS pollution loads at different spatial scales in the Fuxi River basin, China. Data on monitored daily flow rates and concentrations of ammonium nitrogen, total nitrogen, total phosphorus and permanganate index at the sub‐basin and basin scales were collected for a period from 2013 to 2015. Dynamic time warping distance and information measures were used to characterize pollution loads and determine the uncertainties. The results indicate that, at both sub‐basin and basin scales, NPS pollution loads increased nonlinearly with rainfall until it reached 38.4 mm, and subsequently, the NPS pollution loads stabilized. The underlying surface conditions affected the NPS pollution loads more profoundly than rainfall. Additionally, the uncertainty in NPS pollution loads increased with the spatial scales.