Large rivers of the tropics, many of which have extensive floodplains and deltas, are important in the delivery of nutrients and sediments to marine environments, in methane emission to the atmosphere and in providing ecosystem services associated with their high biological productivity. These ecosystem functions entail biogeochemical processes that will be influenced by climate change. Evidence for recent climate-driven changes in tropical rivers exists, but remains equivocal. Model projections suggest substantial future climate-driven changes, but they also underscore the complex interactions that control landscape water balances, river discharges and biogeochemical processes. The most important changes are likely to involve: (1) aquatic thermal regimes, with implications for thermal optima of plants and animals, rates of microbially mediated biogeochemical transformations, density stratification of water bodies and dissolved oxygen depletion; (2) hydrological regimes of discharge and floodplain inundation, which determine the ecological structure and function of rivers and floodplains and the extent and seasonality of aquatic environments; and (3) freshwater-seawater gradients where rivers meet oceans, affecting the distribution of marine, brackish and freshwater environments and the biogeochemical processing as river water approaches the coastal zone. In all cases, climate change affects biogeochemical processes in concert with other drivers such as deforestation and other land use changes, dams and other hydrological alterations and water withdrawals. Furthermore, changes in riverine hydrology and biogeochemistry produce potential feedbacks to climate involving biogeochemical processes such as decomposition and methane emission. Future research should seek improved understanding of these changes, and long-term monitoring should be extended to shallow waters of wetlands and floodplains in addition to the larger lakes and rivers that are most studied.