Physical habitat is the living space of instream biota i.e. all aquatic community, fish community, riparian and instream vegetation. It is a spatially and temporary dynamic entity determined by the interaction of the structural features of the channel and the hydrological regime. Human activities especially sand mining is obstructed instream biota. This study is conducted from upper, middle and lower course in Kangsabati River in West Bengal. Physiochemical parameters were determined by water quality analyzer and species were identified by the field survey in sandchar, mining, and post-mining sites. The result shows that all the deterioration process situated in mining sits and pits but stable ecosystem find out in the entire sandchar sites. Most of the change occurs in the middle course than upper and lower course due to huge mining takes place in the middle course. Therefore, it is a point that mining activities change the aquatic ecosystem.