Abstract: Runoff of nitrogen and phosphorus from farmland is an critical source of river and lake pollution. Organic farming in watersheds could be beneficial for the environment and water quality compared to conventional farming. However, overuse of organic fertilizer can also lead to an increased risk of phosphorus loss. The aim of this study was to analyze the effects of different organic fertilizer application patterns on vegetable yield and nitrogen and phosphorus runoff losses. A field experiment was conducted by building runoff pounds in a vegetable plot in the Songhua Dam watershed, a representative plateau lake in Yunnan Province. Chemical fertilization was the control treatment (CF), and the effects of different organic fertilizer application patterns of cow manure (DMC), chicken manure (CMC), and mixed fertilization of cow manure, chicken manure, and soybean cake (HH) were compared at fertilization rates of 100%, 80%, and 60% of the N input of CF. The vegetable production and nitrogen and phosphorus runoff losses were compared. The dynamic change in total nitrogen (TN) runoff concentration showed that the initial phase (0-25 d) after fertilization was an important period to take preventive and control measures for nitrogen runoff caused by chemical fertilizer application. The results showed that the cumulative concentration of TN in the runoff with organic fertilizer application was significantly lower (26.3%-73.9%) than in the CF treatment after 25 days of fertilization. During the growth stage, the reduction in cumulative concentrations of TN in the runoff was 32.8%-67.0% under organic fertilizer application compared with CF. The cumulative concentration of total phosphorus (TP) in the runoff increased by 49.1% and 12.3% with the DMC and CMC treatments, respectively, but decreased by 15.8%-52.5% under the other organic fertilization treatments. Variance analysis indicated that the nitrogen input levels and the organic fertilzer types could significantly affected the concentration of TN, ammonium, nitrate, and TP in the runoff, and they also had significant interactions with the ammonium nitrogen and TP concentrations. Under 100% N input, the impact of fertilization patterns on TN in the runoff was as follows: CF > DMC > HH > CMC. TP in the runoff was as follows: DMC > CMC > HH > CF. Soil nitrate and available phosphorus were CF > DMC ≈ CMC > HH and CMC > DMC > HH > CF, respectively. Under 60% N input, the reduction of TN and TP in the runoff was significantly greater than 80% and 100% N inputs. The content of soil available phosphorus increased under the organic fertilization treatments compared with CF. Compared with CF and the other types of organic fertilizer, HH significantly increased the yield and quality of broccoli (Brassica oleracea), while the yield of DMC and CMC tended to decrease. On the presumption that broccoli yield increased by 16.7%, the 0.6 HH combination could significantly reduce TN, nitrate, ammonium, and TP in the runoff by 66.5% (18.94 mg·L^-1), 67.2% (11.11 mg·L^-1), 66.2% (6.57 mg·L^-1), and 52.5% (0.5 mg·L^-1), respectively, and could be used as the recommended fertilization system to promote organic vegetable production and to reduce nitrogen and phosphorus runoff losses in the Songhua Dam watershed. The results presented here provide reference and technical support for water quality protection through organic agriculture in China.