Tropical primary forests have been disappearing quickly to make use of the land for commercial purposes. Land-use change has an impact on downstream aquatic processes, but those impacts have mainly been studied in temperate climate regions. The present article reviews the impacts of various tropical land-use changes caused by human activities on downstream riverine and estuarine water properties and biogeochemical cycles, focusing especially on the behaviors of nitrogen (N) and phosphorus (P). Logging of tropical primary forests, subsequent establishment of pasture lands, and occasional wildfire or intentional burning have decreased terrestrial N fixation and increased the discharge of P combined with soils, which has lowered the N:P ratio of dissolved inorganic nutrients in the adjacent stream waters and downstream rivers. Agricultural fertilizers and aquacultural practices basically cause nutrient enrichment in downstream riverine and estuarine waters, changing the N:P ratio depending on the source. Finally, urbanization causes eutrophication in many tropical estuaries, where a halocline forms easily because of a warm temperature throughout the year and the water at the bottom of the estuary tends to become hypoxic or anoxic. Overall, the impact of land-use change on aquatic processes may be more serious in tropical regions than in temperate or cold climate regions because of (1) a higher biomass and nutrient stock in original tropical forests; (2) higher precipitation, more frequent episodic flooding, and warmer temperatures in tropical regions; and (3) certain practices that are rapidly expanding in tropical regions such as land-based aquaculture. Various land-use changes are causing downstream nutrient enrichment or disturbance of the nutrient balance at tropical land-sea interfaces, and the overall N:P ratios in the aquatic ecosystem seem to be declining. Nonetheless, if proper management is conducted and the discharge of nutrients and soils ceases, tropical aquatic systems may have the potential to recover faster than those in other climate regions because of their abundant precipitation and warm temperature. Long-term monitoring and more attention to elemental stoichiometry are important areas for future research.