Tropical ecosystems offer a unique setting for understanding ecohydrological processes, but to date, such investigations have been limited. The purpose of this paper is to highlight the importance of studying these processes—specifically, how they are being affected by the transformative changes taking place in the tropics—and to offer an agenda for future research. At present, the ongoing loss of native ecosystems is largely due to agricultural expansion, but parallel processes of afforestation are also taking place, leading to shifts in ecohydrological fluxes. Similarly, shifts in water availability due to climate change will affect both water and carbon fluxes in tropical ecosystems. A number of methods exist that can help us better understand how changes in land use and climate affect ecohydrological processes; these include stable isotopes, remote sensing, and process-based models. Still, our knowledge of the underlying physical mechanisms, especially those that determine the effects of scale on ecosystem processes, remains incomplete. We assert that development of a knowledge base concerning the effects of transformative change on ecological, hydrological, and biogeochemical processes at different spatio-temporal scales is an urgent need for tropical regions and should serve as a compass for emerging ecohydrologists. To reach this goal, we advocate a research agenda that expands the number and diversity of ecosystems targeted for ecohydrological investigations and connects researchers across the tropics. We believe that the use of big data and open source software—already an important integrative tool/skill for the young ecohydrologist—will be key in expanding research capabilities.