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Water hyacinth is able to sequester large amounts of carbon dioxide (CO2) in wetlands. At the same time, the high production of organic matter combined with the plant's capacity to limit the diffusion of oxygen from the atmosphere into the water creates favorable conditions for the production of methane (CH4). The combination of these mechanisms challenges the prediction of water hyacinth's net effects on greenhouse gas (GHG) emissions. To unravel the impact of water hyacinth on GHG fluxes, we performed an extensive fieldwork study encompassing 22 sites dominated by water hyacinth in the Pantanal and Amazon during two different seasons. The highest CH4 emissions from water hyacinth beds occurred in shallow systems where sediment rooting enabled plant-mediated CH4 transport (307 ± 407 mg CH4 m−2 day−1 in waters shallower than 1 m, as opposed to 6.1 ± 10.6 mg CH4 m−2 day−1 in deeper waters). When CO2 uptake rates are added to the GHG budget (in terms of global warming potential), the water bodies were usually a GHG sink (− 5.2 ± 10 gCO2 eq m−2 day−1). The strength of the sink is highest in deeper systems where even a low water hyacinth coverage may already offset open water emissions. This dual effect of strong CO2 uptake—and at least temporal carbon storage in biomass—in combination with a high CO2–to-biomass-to-CH4 (and possibly back to CO2) conversion highlights the necessity to include vegetation characteristics in relation to depth when estimating GHG fluxes for tropical wetlands. [ABSTRACT FROM AUTHOR]