Tropical rivers and their floodplains are some of the most productive ecosystems in the world, but they are under increasing threat from human modification of their flow regimes and ecology. Furthermore, tropical regions cover 36% of Earth’s landmass and comprise most of the world’s river channel length, but less than 3% of all published research in freshwater ecology has focused on tropical regions. This lack of basic research inhibits our ability to predict how human modification of tropical freshwaters will affect their ecological functioning. In this study, we reviewed all global research on tropical freshwater food webs to identify the spatial and conceptual knowledge gaps. We used previously published research on general principles for Australian tropical aquatic food webs to structure our review and grouped studies using the United Nations Geoscheme. Of the 2,825 papers included in our systematic review, we found that the spatial distribution of tropical food-web research is biased towards South America, Australia and Central America, with more than 65% of the research conducted in these regions. Although aquatic ecosystems in Southeastern Asia are arguably most at risk from immediate and future human modifications, less than 6% of all tropical food-web research has been conducted in this region. Over 75% of studies focusing on the primary sources of energy supporting food webs and trophic dynamics was undertaken in just four regions: South America, Central America, the Caribbean and Australia. There was overwhelming support for the importance of temporal, longitudinal and lateral hydrological connectivity for the provision of cross-system food-web and ecosystem process subsidies. Very few studies documented the importance of vertical hydrological connectivity for aquatic food webs in tropical regions. We propose an updated set of general principles describing river and wetland food webs to inform management in the world’s tropical regions.