Abstract. Under the background of climate change and human's activities, there has been presenting an increase both in the frequency of droughts and the range of their impacts. Droughts may give rise to a series of resources, environmental and ecological effects, i.e. water shortage, water quality deterioration as well as the decrease in the diversity of aquatic organisms. This paper, above all, identifies the impact mechanism of drought on the surface water quality of the basin, and then systematically studies the laws of generation, transfer, transformation and degradation of pollutants during the drought, finding out that the alternating droughts and floods stage is the critical period during which the surface water quality is affected. Secondly, through employing indoor orthogonality experiments, serving drought degree, rainfall intensity and rainfall duration as the main elements and designing various scenario models, the study inspects the effects of various factors on the nitrogen loss in soil as well as the loss of non-point sources pollution and the leaching rate of nitrogen under the different alternating scenarios of drought and flood. It comes to the conclusion that the various factors and the loss of non-point source pollution are positively correlated, and under the alternating scenarios of drought and flood, there is an exacerbation in the loss of ammonium nitrogen and nitrate nitrogen in soil, which generates the transfer and transformation mechanisms of non-point source pollution from a micro level. Finally, by employing the data of Nenjiang river basin, the paper assesses the impacts of drought on the surface water quality from a macro level.