The Lower Indus reaches – Guddu and Sukkur – are among the most complicated areas in terms of reach migration. Both climate change and human activities in recent periods along with pond system operation accelerated riverine channel morphology. A GIS-based approach using multi-temporal Landsat images (1986–2020) was employed to characterize the morphometric parameters. Results showed that width of the study reaches varied from 2.1 to 12 km. The braiding index (BI) value for Guddu reach varied from 3.47 to 7.18, and BI value for Sukkur reach varied from 2.11 to 4.92. It is observed that no erosive activity of banks occurred for peak runoff value of <5,880 m3s−1. The sediment load during low flow (LF) period was estimated to be 0.715 million tons/day which comprised 77% fine sediment and 23% sand. The sediment load during high flood (HF) period was about 1.296 million tons/day. The median size (D50) of bed material during the HF period was 0.101–0.206 mm and during LF period was <0.0625 mm. The rough set theory (RST) showed that velocity, shear stress, slope, runoff, and sediment load factors are majorly causing the river shape changes. This study is a standpoint of planning flood recovery, riverine regulations, and navigation safety.