This paper explores the ecological effects of the top-down Ganges Basin water management systems in Chapra, Bangladesh, based on my ethnographic fieldworka data collected in 2011-12. An example of this top-down system is the Farakka Barrage in India that causes major ecological system failures and challenges to community livelihoods. The reduction in Ganges Basin water flow in Bangladesh based on the pre and post Farakka comparison is helpful in understanding these failures and their effects on community livelihoods. My argument is that basin communities are capable of becoming empowered by Ganges Basin water management and failures in the management create major challenges to the livelihood of these communities. In this context, I analyze the current Ganges Basin management practices, focusing specifically on the Joint River Commission and the 1996 Ganges Treaty between India and Bangladesh, and their effects on the basin communities in Chapra. My fieldwork data point out that the current shortcomings in basin management can be overcome with an improved management system. Water governance based on a multilateral approach is a way to restore the basin’s ecological systems and promote community empowerment. Based on this empowerment argument, this paper is divided into the following major sections: importance of the basin ecosystems for protecting community livelihoods, limitations of current basin management practices and community survival challenges, and proposed water governance for community empowerment.