In this paper, an attempt has been made to document consequences of river sand mining on water quality and instream biota in an alluvial channel as Kangsabati River, India. Water Quality Index (WQI) is used to identify the adverse effects of water quality on species diversity, richness, and evenness of the aquatic community. Physicochemical parameters (PP) such as pH, dissolved oxygen, total dissolved solids, electric conductivity, salinity, biological oxygen demand, magnesium cation, and turbidity are analyzed from 27 representative sampling stations as sandchar, mining, and pit sites along the upper, middle, and lower course. Pearson correlation indicates that pH and magnesium cation is the most significant parameters with WQI. Principal component analysis denotes good water quality ( 70) water qualities are presence in mining and pit sites. Applying Simpson’s index, Simpson’s index of diversity, Simpson’s reciprocal index, and Shannon–Wiener diversity index on instream biota, those vary from sandchar (0.19, 0.81, 5.57, and − 1.34) to mining (0.11, 0.89, 9.23, and − 1.39) and pit sites (0.12, 0.90, 10.68, and − 1.50). Maximum Margalef’s index of species indicated the richness of species types in mining sites (4.62), with minimum mean values in sandchar sites (3.64). Contrastingly, Pielou’s evenness index is high in sandchar sites (− 1.05) and low in mining sites (− 1.49). Therefore, significant physicochemical parameters such as PH, dissolved oxygen, magnesium cation, and electric conductivity changes the diversity index, species richness and evenness in mining and pit along the middle and lower courses caused by sand mining.