Huangshui River (HSR) is the mother river of Qinghai province. Croplands and grasslands cover more than 76% of the total area, and highland agriculture and animal husbandry are the dominant industries. The use of pesticides, fertilizers, and feed additives increases the risk of heavy metal (HM) contamination. In this study, the concentration of HMs in the main stream and tributaries of HSR were investigated. The Positive Matrix Factorization model was used for source apportionment, and Health Risk Assessment method was used to assess the human health risks. To further analyze the effect of agriculture and animal husbandry on aquatic environment and human health, we considered agriculture and animal husbandry as two factors in the source apportionment process, defined the effect of the factors, established the calculation formula, and quantified the effects. The results show that the overall situation of aquatic environment in HSR is good; natural processes, traffic tail gas and atmospheric deposition, agricultural planting, industrial wastewater discharge, and animal husbandry are the main sources of HMs in the water. These HMs present noncarcinogenic and carcinogenic risks for infants. A total effect of agricultural and animal husbandry on HMs or HI in HSRB is approximately 20%, while on TCR is 40%. However, the effects of agriculture on the hazard quotient of arsenic, carcinogenic risk of nickel and lead, and that of animal husbandry on carcinogenic risk of cadmium were significant. This study can provide a theoretical basis for local managers of agriculture and animal husbandry to perform their work effectively.