Assessments of the spatiotemporal distribution of livestock manure and its risk to the watershed are important to prevent water pollution. In this work, the spatiotemporal livestock manure distribution and its risk for the Chaohu lake basin were evaluated based on the excretion coefficient method and ArcGIS technology. In detail, the amounts of livestock manure and its associated pollutants, including chemical oxygen demand (COD), five-day biochemical oxygen demand (BOD5), ammonia (NH4+-N), total nitrogen (TN), and total phosphorus (TP), were calculated from 2009 to 2019. Then, the diffusion concentrations of COD, BOD5, NH4+-N, TN, and TP and the water pollution risk index from livestock manure were estimated and predicted for the Chaohu lake basin. The results indicated that the mean amount of livestock manure had reached 1.04 × 107 t in the Chaohu lake basin in the studied decade. The COD, BOD5, NH4+-N, TN, and TP from livestock manure in Feixi and Feidong contributed 54.26% and 54.40% of the total in the whole basin. These results demonstrate the potential pollution risk of livestock manure for the Chaohu lake basin. Moreover, the diffusion concentrations of COD, BOD5, NH4+-N, TN, and TP for the lake basin were from highest to lowest as follows: Feixi > Feidong > Chaohu > Lujiang > Wuwei > Shucheng > Hefei. The water pollution risk index was more than 20 in Feixi and Feidong, indicating that these areas were heavily affected by local livestock manure. The water pollution risk index will be approximately 18 for the Chaohu lake basin in 2030, implying that the Chaohu lake watershed will suffer moderate pollution from animal manure. These results provide scientific support for policymakers to enhance manure utilization efficiency and control livestock manure loss, causing water eutrophication in Chaohu lake basin or other similar watersheds.