Abstract: Nitrogen and phosphorus loss in surface runoff from farmlands has been the main cause of water eutrophication.Fujian Province is one of the regions with the highest intensity of fertilizer application per unit area of land in China.The subtropical monsoon climate zone and hilly region with heavy summer and autumn rains on steep hill-slope farmlands in Fujian increase the risk potential for pollution.Thus to analyze current conditions and characteristics of nitrogen and phosphorus loss in surface runoff from farmland in Fujian Province, we selected nine prefectural level cities in Fujian Province as the study areas to estimate the loss of nitrogen and phosphorus in surface runoff in farmlands based on investigated data of fertilizer use in the cities for the period from 1985 to 2016.By integrating the three factors of pollution risk (fertilizer loss, rainfall and drainage intensity), we evaluated nitrogen and phosphorus pollution risk from farmland fertilizer to determine critical areas of primary concern.We used the ArcGIS platform to make thematic maps for visualizing the spatial distribution of contaminated areas by nitrogen and phosphorus.The results showed that fertilizer application in Fujian Province increased during the 30-year period from 4.911×10⁵ t to 1.239×10⁶ t, with an annual average rate of increase of 3.03%.The amount of fertilizer use in Fujian Province was highest (1.243×10⁶ t) in 1999, accounting for 3.01% of total fertilizer use in China.The intensities of nitrogenous and phosphate fertilizer use in Zhangzhou City were largest, with respective values of 880.40 kg·hm^-2 and 429.21 kg·hm^-2.The high nitrogen and phosphorus surface runoff were concentrated in Zhangzhou City, which were respectively 1.571×10⁶ t and 3.590×10⁵ t, with nitrogen and phosphorus loss intensities of 8.71 kg·hm^-2 and 1.99 kg·hm^-2.However, pollution risk values of nitrogen and phosphate fertilizer were highest in Nanping City, reaching respectively 63.19% and 63.37%-a high risk of nitrogen and phosphorus pollution.Xiamen City had the lowest risk values, respectively 0.53% and 0.53%.The others were in between and in the following decreasing order:Ningde City (57.22% and 54.48%) > Sanming City (53.34% and 53.34%) > Longyan City (51.38% and 51.20%) > Zhangzhou City (46.73% and 46.73%) > Quanzhou City (45.49% and 40.25%) > Fuzhou City (34.35% and 33.80%) > Putian City (18.59% and 16.93%).By using cluster analysis, these nine cities were divided into three groups-heavy to moderate pollution risk (Sanming City, Longyan City, Ningde City and Nanping City), moderate to light pollution risk (Quanzhou City, Zhangzhou City and Fuzhou City) and low pollution risk (Xiamen City and Putian City).We concluded that Zhangzhou City needed to emphasize on reducing nitrogen and phosphorus fertilizer use in agriculture.Nanping City needed to hammer at risk control of nitrogen and phosphorus loss in farmlands.The others cities needed to strengthen the development of ecological agriculture to facilitate the construction of Fujian Experimented Region of Ecological Civilization and the promotion and optimization of control measures of nitrogen and phosphorus loss in surface runoff.