Abstract: To study the relationship between aquatic organisms and environmental indexes in the interlaced areas of agriculture and animal husbandry in Qinghai, diversity of benthic macroinvertebrates and physical and chemical indexes were investigated at 47 sampling sites in the upstream of Huangshui River in April (dry season) and August (rainy season) of 2015. In the sampling sites, water physical indexes of Huangshui River were determined by multiparameter water quality tester and FP311 bar-type flow meter. And water chemical indexes were tested in the laboratory. The contents of total nitrogen and total phosphorus were determined by ultraviolet spectrophotometry of potassium persulfate oxidation, the content of NH4 -N were determined by Nessler’s reagent spectrophotometry, and benthic macroinvertebrates were collected by Sauber’s net and D-shaped net. The results showed that the physical and chemical indexes in the branch stream of Huangshui River were better than that of the trunk stream, especially the turbidity, proportion of fine sand, contents of NH4 -N, TN and TP. There were a total of 59 species of the macro-invertebrates in 57 genera, 28 families. Among them, 4444 individuals of 54 species were belonged to 7 orders of Insecta, accounting for 91.5% of all species and 76.4% of the total individuals. Individuals in Crustacean, Mollusca and Oligochaeta occupied 23.6% of the total individuals. The average number of total taxa of benthic macroinvertebrates in the branch stream of Huangshui River was 6.76, which was not far from that in the trunk stream (8.14); the average number of total taxa of EPT in the branch stream of Huangshui River was 3.36, which had not obvious difference compared with that of the trunk stream (2.48). However, the species number of the pollution-tolerant macroinvertebrates in the trunk stream was larger than that in the branch stream, and the species number of the pollution-sensitive macroinvertebrates in the branch stream was larger than that in the trunk stream. The results indicated that water quality in the branch stream of was better than that of the trunk stream, and the difference was caused by the heavier pollution in the trunk stream.