<p>Water and nutrient loss in the black soil region of Northeast China poses a serious threat to food security. By collecting soil, leachate, and rainfall runoff samples, the impact of farmland surface drainage system was examined. By the end of crop growth season, the contents of total carbon (TC), total nitrogen (TN), total phosphorus (TP), and total potassium in the topsoil of test plot increased by 2.65%, 3.90%, -0.05%, and − 2.75%, respectively, while those of check plot changed by -9.35%, -7.8%, -21.1%, and − 3.3%. Additionally, the contents of available nitrogen, phosphorus, and potassium in the topsoil of test plot rose by 50.1%, 3.0%, and 24.6%, respectively, while those of check plot changed by 48.9%, -51.6%, and − 14.1%. The concentrations of TC, TN, and TP in the leachate from the test plot were 8.4%, 43.3%, and 30.6% lower than those from the check plot, respectively. The crop yield in the test plot increased by 3% compared with that in the check plot. The concentrations of lost nutrients in surface runoff gradually increased with prolonged runoff duration, including different forms of carbon and nitrogen, as well as TP and total suspended solid. Organic carbon and nitrate nitrogen were the main forms of lost carbon and nitrogen in surface runoff, respectively. These results indicated that the surface drainage system could reduce the nutrient loss of topsoil driven by rainfall, and preserve soil nutrients and productivity. This study provides a viable roadmap for water and nutrient conservation in the study region.</p>