The Ganges–Brahmaputra estuary, located in the northern Bay of Bengal, is situated within the largest delta in the world. This river basin features a complex river system, a dense population, and significant variation in watershed vegetation cover. Human activities have significantly impacted the concentration of total suspended matter (TSM) in the estuary and the ecological environment of the adjacent bay. In this study, we utilised the Landsat series of satellite remote sensing data from 1990 to 2020 for TSM retrieval. We applied an atmospheric correction algorithm based on the general purpose exact Rayleigh scattering look-up-table (LUT) and the shortwave-infrared (SWIR) bands extrapolation to Landsat L1 products to obtain high-precision remote sensing reflectance. In conjunction with the normalised difference vegetation index (NDVI), precipitation, and discharge data, we analysed the variation and influencing mechanisms of TSM in the Ganges–Brahmaputra estuary and its surrounding areas. We revealed notable seasonal variation in TSM in the estuary, with higher concentrations during the wet season (May–October) compared to the dry season (the rest of the year). Over the period from 1990 to 2020, the NDVI in the watershed exhibited a significant upward trend. The outer estuarine regions of the Hooghly River and Meghna River displayed significant decreases in TSM, whereas the Baleswar River, which flows through mangrove areas, showed no significant trend in TSM. The declining trend in TSM was mainly attributed to land-use changes and anthropogenic activities, including the construction of embankments, dams, and mangrove conservation efforts, rather than to runoff and precipitation. Surface sediment concentration and chlorophyll in the northern Bay of Bengal exhibited slight increases, which means the limited influence of terrestrial inputs on long-term change in surface sediment concentration and chlorophyll in the northern Bay of Bengal. This study emphasises the impact of human activities on the river–estuary–coast continuum and sheds light on future sustainable management.