Forested riparian zones are known to reduce movement of nitrogen from farms into streams in temperate areas, but predictive models of nitrogen transport and transformations rely on hydrological understanding, which is limited in the humid tropics. As a first step to understanding nitrogen cycling in the forested riparian zone of a lowland humid tropical agricultural landscape, we studied the hydrology of a riparian site in northeast Australia. The site has undulating topography and a 150-m wide strip of relatively undisturbed forest between sugarcane fields and the perennial stream. Riparian hydrology was dynamic in the wet season with frequent interactions between ground and surface water. Vertical and lateral fluxes of water through the variably saturated zone were high during the wet season due to intense rainfall, permeable soils and a variable discharge zone. However, complete saturation was never observed in the variably saturated zone. During the dry season groundwater movement was slow and the water table was several metres deep throughout most of the site. Uptake of groundwater by vegetation was a significant component of the water balance during the dry season and groundwater discharge to the creek is likely to be negligible at this time. During the wet season, uptake was small relative to other fluxes and the transpiration requirements of the trees could be met by the topsoil for much of the time. The hydrological conditions encountered are likely to exert large and variable influences on the transport and transformations of nitrogen in this part of the landscape. Contrary to the common understanding of riparian zone function, it appears that riparian zones of humid tropical lowlands are likely to be ineffective at removing nitrogen from groundwater. This will have implications for downstream water quality and ultimately on the quality of water discharging into the Great Barrier Reef lagoon, a sensitive and vulnerable marine environment.