This chapter deals with the hydrobiological assessment of the Mahananda System. However, in this study, only the fish assemblageFish assemblage has been studied in the view that fishes are on top of the food chain of the natural flowing system. The dataset used in this study is mostly field-based. From July 2019 to December 2020, for 6 times fishes are collected from 5 sampling sites solely at the unconfined reaches. The fish assemblage of the confined reaches is not assessed due to incompetency in fishing at high-velocity streams. Several indices are selected regarding the assessment of community structureCommunity structure, trophic level and habitat orientation as well as the diversity indices such as richness, dominance and evenness of the fish species found in both rivers. Furthermore, a temporal change between the fish species found during this study and by Paul et al. (Rec Zool Surv India 109(4):15–23, 2009). has been assessed. It is understood as the results revealed there is almost no spatial variability regarding the diversity indices, however, some inter-seasonal variability can be observed. The confluence point of Mahananda and Balason is observed with the highest species richnessSpecies richness and diversity. The decrease in species richness between Paul et al. (Rec Zool Surv India 109(4):15–23, 2009). and this study is alarming and the richness of edible fishEdible fish species is replaced by increasing invasive ornamental fish species despite heavily degraded water quality.