The Ganges, Brahmaputra and Meghna rivers are the three main rivers contributing to the formation the GBM (Ganges–Brahmaputra–Meghna) delta system. The delta system undergoes several environmental challenges both natural and manmade. A significant portion of population from different nations is directly and indirectly dependent on these three rivers for their sustenance. As transboundary rivers, they suffer a lack of transnational cooperation in terms of river protection and sustainable management. This review article analyses the environmental challenges in the GBM delta system to better understand the critical issues related to sustainable delta management. It also focuses on the transboundary issues and their solutions through cooperation, knowledge sharing and other joint activities between nations. The Ganges, Brahmaputra and Meghna rivers suffer from different forms of pollution. Significant sources include domestic, industrial and agricultural affluents along with direct defecation, bathing, washing, solid waste dumping and throwing of ritualistic burnt dead bodies into river water. The level of pollution creates havoc in aquatic ecosystem and leaves the water unusable for humans as well. The significant growth of population in these regions has modified the land cover of the GBM delta system. The rise in agricultural land, dams and other hydraulic structures has modified the erosion and sedimentation dynamics of the Ganges, Brahmaputra and Meghna rivers. As a result, the cases of riverbank erosion, riverbed siltation and river course shifting are also rising. The rivers also struggle with the various types of natural disasters like cyclones, storm surges, floods, droughts, salinity intrusions, coastal erosions and tidal bores. There is also a lack of understanding and cooperation between countries when it comes to sustainable delta management. To top it off, other issues like extreme poverty, lack of education, dependency on nature-based agricultural practices have also clouded the long-term development of the delta system and its people. The above-mentioned challenges require holistic and integrated action plans among respective nations. This can be achieved through effective policy dialogues, transnational protection and conservation plans, information sharing, co-learning, joint research programs, transstate accountability and technological advancements which can be ensured by each of the participating nations. The Ganges–Brahmaputra–Meghna (GBM) delta system extends for more than hundreds of kilometres along the Bay of Bengal coastline. The Ganges and Brahmaputra River drains roughly around 75% of the Himalayan mountain range. These two rivers carry around 1.1 GT/yr of sediment and dump on the Bengal Basin. This amount is equal to around 6–8% of the total sediment input dumped on the oceans globally. These rivers are extensively affected by different types of pollutions, erratic flood intensities and altering tidal characteristics. They also suffer from river stage fluctuations in the downstream riparian regions due to the construction and operation of hydraulic structures in the upstream regions. This study provides a critical analysis of the present issues and challenges regarding the active rivers of the GBM delta system and recommends a holistic and sustainable management plan for the protection and conservation of the rivers by analysing previously published research works and secondary datasets. The Ganges, Brahmaputra and Meghna river basins experience various point and non-point pollutions. The downstream regions face a higher rate of pollution than the upstream ones. As the rivers approach the delta mouth, land use patterns and land covers change due to increased rate of urbanization, industrialization, agricultural practices and climate change effects. Their flow is also being controlled by several upstream hydraulic structures like dams, barrages and reservoirs. Consequently, the river basins face many natural and anthropogenic disasters. The combined effect of these issues elevates the vulnerability of the downstream delta mouth population and destabilizes their socio-economic conditions. These crises can be solved through transnational cooperation, regional capacity building and sharing of information between upstream and downstream riparian countries. Inclusive and flexible strategies with appropriate policy dialogue may lead to amendments of current agreements which may eventually create a sustainable platform to overcome the environmental challenges of the Ganges–Brahmaputra–Meghna delta system.KeywordsGBM deltaGanges RiverBrahmaputra RiverMeghna RiverPollutionLand useDisasterClimate changeTransboundary riverCooperationManagement