Halda, one of the major tributaries of the mountainous river Karnaphuli, is well known as the country’s only natural carp spawning ground. However, the river habitat is under constant threat due to human interventions like loop cutting, pollution from the paper mill and power plant, blocking natural water flow of larger tributaries by introducing sluice gates, embankments and rubber dam over the river at upstream, as well natural causes like siltation, erosion and climate change impacts. A study is conducted to address the issues of the ecosystem, sustainable management and the flow regulation impacts of dams in the Halda River. In this research, a hydrologic model ArcSWAT has been built to assess the contribution of rainfall on the river discharge to be used as output from the tributaries in the hydrodynamic model Delft3D. The research findings help us to perceive the effect of the dams on fish breeding condition in the river. Also, this study presents the trends of channel flow against human interventions and proposes an adaptation plan through a public–private Partnership (PPP) model to overcome the existing deteriorating condition of the Halda River. The planform analysis showed the encroachment of the river impacting the river bends, significant for aquaculture over the last three decades, whereas the stage trends showed the low availability water scenario in these four locations of the river stretch. Conservation of the Halda River is a national priority due to its unique ecological and commercial importance, and it is expected that the proposed PPP framework will ensure the long-term sustainability of the river ecosystem.