Tropical ecosystems are epicentres of biodiversity and play key roles in global biogeochemical cycles, for example in the sequestration of terrestrial and coastal carbon. Tropical coasts are characterised by large river systems delivering huge amounts of material into the coastal ocean, with fluvial inputs of nutrients, carbon, and sediment from tropical rivers playing a globally significant role. The majority of the population in tropical regions lives along these rivers and coasts and depends economically on aquatic resources. Yet rapid development in many tropical regions, such as Borneo, is causing large-scale impacts on riverine and coastal ecosystems, the biogeochemical consequences of which remain poorly known. Interestingly, it has been suggested that coastal systems in tropical regions react differently to anthropogenic stresses compared to coasts in temperate and subtropical regions. However, our understanding of tropical rivers, estuaries, and coasts is still too basic to predict the impacts of increasing anthropogenic pressures. An improved understanding of these ecosystems and their biogeochemistry is therefore urgently needed. This special issue calls for work that examines biogeochemical processes of tropical rivers, estuaries, and coasts as well as their response to environmental change and the interplay of natural and anthropogenic control factors.