Flow modification pursuing dams is widely found. Some works also focused on its impact on floodplain wetland hydrology. However, how this change can pose an impact on habitat conditions, ecological conditions, and trophic state is also a matter of investigation. The very least attention has been paid to this so far. Therefore, the present study focused on these, taking the dam-induced Lower Tangon river basin of India and Bangladesh as a case. The degree of flow alteration in the river was presented in a heat map. Multi-parametric machine learning (ML) approaches were applied to model hydrological instability and habitat condition. The ecological consequences like evaluating eco-deficit using flow duration curve (FDC) approach, trophic state using trophic state index (TSI), fish habitat zone using image-based hydrological parameters, etc. were measured. The study exhibited that after damming, the degree of river flow modification was about 41%. Consequently, the wetland hydrological instability and habitat conditions were degraded. In the post-dam period, > 50% of wetland area was lost, and hydrological instability was enhanced considerably over wider parts of the wetland. Habitat conditions of the existing wetland also witnessed fragility (poor and very poor areas increased by about 22.23 and 9.34%). As a result of this, adverse ecological responses were found. For instance, the eco-deficit area was increased by 36.19%, a good proportion (100%) of wetlands was witnessed the transformation of TSI from oligotrophic to mesotrophic state, and optimum fish habitat area was declined. The ecological strength map integrating all the cause-effect model parameters showed that good ecological strength was reduced from 49 to 2% in the post-dam. The result of the study would be very useful for wetland restoration for ecological and human well-being.