Increasing advancement in development activities in the Indian Himalayan region in tandem with changing climate is influencing the ecological patterns of rivers. Thus, the present study investigates the effect of various degrees of anthropogenic stresses and possible implication of thermal dynamics of river water on the macroinvertebrate community in the Mandakini River, which flows in the vicinity of Kedarnath Wildlife Sanctuary of Chamoli district, Uttarakhand. The main objective was to study the community structure of macroinvertebrates in the Mandakini River and to calculate the effect of anthropogenic stresses on the macroinvertebrate community, particularly on Ephemeroptera, Plecoptera, and Trichoptera. The study was carried out in 10 spatially located sampling stations, and the frequency of sampling was divided into pre-and post-monsoon season (May and November 2017). Based on the degree of anthropogenic stresses, sampling locations were divided into least (Sonprayag), medium (Ukhimath), and high disturbed (Rudraprayag) sites. A total of 3257 individuals belonging to 7 orders and 21 families were found in both the sampling season. Diptera and Trichoptera were dominant orders in both the seasons, whereas Baetidae (Ephemeroptera), Hydropsychidae, Leptoceridae (Trichoptera) and Chironomidae (Diptera) were dominant families. Shannon diversity index varies from 2.048 to 2.25 in the least disturbed site (Sonprayag), 0.186-2.446 in medium disturbance (Ukhimath), and 1.362-2.271 in the highly disturbed site (Rudraprayag) in both the sampling season. Quantification of the EPT index shows a negative trend with an increase in anthropogenic stress, and it was least in Rudraprayag as compared to the other two sites. Result of one-way ANOVA shows a significant difference in diversity between pre-and post-monsoon season (p < 0.05). Analyzing the research gaps, it is recommended to have long-term ecological monitoring of high altitude and glacier-fed rivers and streams to obtain robust information regarding the dynamics of the riverine ecosystem in Garhwal Himalayas.