This study aimed to clarify the characteristics of soil nutrient accumulation and the potential risk to non-point pollution in the basin under eroded environment and long-term fertilizer application on farmland. In table-gully region of the Loess Plateau, soil and sediment samples were collected to analyze the size distribution and C, N, P contents in aggregates and the potential environmental risks in different erosion landforms from Tableland-Slope-Gully system (TSG) and Flatland-Washland-Waterstead system (FWW). The results showed that:(1) The highest weight percentage of small aggregate (< 63 μm) was found in low-lying areas, such as gully and waterstead, and FWW system was significantly higher than TSG system. (2) The contents of SOC, TN, TP, Olsen-P in Tableland were 8.49, 1.19, 1.23 g/kg and 51.80 mg/kg, respectively, which were 1.39, 1.49, 1.76 and 16.27 times of the recorded in the early 1980s; and 6.80 g/kg, 1.00 g/kg, 1.07 g/kg, 27.40 mg/kg for Flatland, respectively, which were 1.12, 1.25, 1.52 and 8.13 times of the recorded in the early 1980s. Moreover, soil phosphorus was accumulated most significantly among all soil nutrients. The SOC, TN, TP, Olsen-P contents in different aggregates showed the same decreasing pattern as follow > 250, 63~250, < 63 μm. (3) The SOC, TN, TP, Olsen-P were significantly reduced along the erosion topographic units under TSG and FWR systems; additionally, soil phosphorus contents in 63 μm aggregate at gully and waterstead plots increased to the value of tableland in the early 1980s. The characteristics of aggregates (< 250 μm) distribution and the mutation point of CaCl₂-P were prominent, and became the potential risk source for the water environment effected by the accumulation of soil nutrients under TSG and FWR systems. Therefore, preventing soil erosion and improving fertilization measures are the basis for ensuring high-quality development of the Yellow River basin.