A good number of researchers investigated the impact of flow modification on hydrological, ecological, geomorphological conditions in a river. A few works also focused on hydrological modification on wetland with some parameters but as far the knowledge is concerned, linking river flow modification to wetland hydrological and morphological transformation following an integrated modeling approach is almost absent. The current study aimed to explore the degree of hydrological alteration in the river and its effect on downstream riparian wetlands adopting advanced modeling approaches. After damming maximally 67 to 95% hydrological alteration was recorded in respect to maximum, minimum, and average discharges. Wavelet transformation analysis figured out a strong power spectrum after 2012 (damming year). Due to attenuation of flow, the active inundation area was reduced by 66.29%. After damming, 524.03 km2 (48.97% to total pre-dam wetland) was completely obliterated. Hydrological strength (HS) modeling also reported areas under high HS was declined by 14% after post-dam condition. WSS and HS matrix, a new approach, used to feature wetland coupling inundation connectivity and current hydrological state. HS under critical and stress wetland hydrological security zones deteriorated in the post-dam period. The morphological transformation was also well recognized showing an increase of area under the patch, edge, and decrease of the area under large core area. All these findings established a good linkage between river flow modification and wetland transformation and it provided a good clue for managing wetland.