Abstract: In order to fully understand the current situation of livestock and poultry farming pollution and its potential impacts on the ecological environment, the potential of livestock and poultry manure as a substitute for fertilizers was analyzed in the source area of the middle route of the South-North Water Transfer Project. The environmental risk assessment model was used to quantitatively analyze the main manure source structure of each county in 2022 based on the data of 49 county-level livestock and poultry farming quantities and arable land area. The total nutrient content and organic fertilizer substitution potential of livestock and poultry manure of different species and in different regions were estimated. The results showed that the total amount of livestock and poultry manure was 1534.02×10⁴ t, and the distribution was relatively concentrated. The amount of chemical oxygen demand (COD) was the highest (199.42×10⁴ t), followed by total nitrogen (TN, 8.6×10⁴ t), and total phosphorus (TP) production was less (1.77×10⁴ t). 18.37% of the counties in the water source area had a potential pollution risk of livestock and poultry breeding, among which Danfeng County was at medium risk; Neixiang County and Maojian District were at risk; Dengzhou City, Danjiangkou City, Yunyang District, Xunyang County, Shanyang County, and Wanyuan City were at a little risk; and the rest were at a safe level. The load of animal excretion per hectare of arable land in the water source area was 9.235 t hm⁻², the alarm value was 0.308, and the grade index was I. The total equivalent standard pollution load was 48.165×10¹⁰ m³. The source structure of pollution was inconsistent in different regions. TP was the primary pollutant in livestock and poultry farming, and its equivalent standard pollution load accounted for 36.69% of the total load, followed by TN with a pollution load rate of 35.71%, and COD with the lowest equivalent standard pollution load rate of 27.60%. Livestock and poultry pollution in the water source area mainly originated from pigs and cattle, whose contributioned to the total equal pollution load reached 47.90% and 41.77%, respectively. The total nutrient resource of manure in the water source was 21.195×10⁴ t, and the theoretical potential for fertilizer substitution was 20.67%. According to the theory of nutrient resources for different livestock and poultry manures, the potential to replace fertilizer was cattle manure (8.86%) > pig manure (6.50%) > poultry manure (3.05%) > sheep manure (2.26%). The theoretical potential of nitrogen, phosphorus, and potassium in animal manure to replace fertilizer was 16.77%, 6.89%, and 42.23%, respectively. It is of great significance to control the total livestock and poultry production in potential risk areas, promote structural adjustment in different counties, and realize the resource utilization of livestock and poultry manure instead of fertilizer to promote the green development of the South-North Water Transfer Project aquaculture industry.