•Stream nitrate loads were proportional to area of agriculture drained.•Inter-stream differences were due to groundwater flow and riparian cover.•Longitudinal profiles of water quality are critical to comparing streams.•It is necessary to understand hydrology to gauge riparian effects on streams.•N contamination can be adequately mitigated only by reducing fertilizer use. We measured water quality along four Australian tropical streams in two catchments with similar agricultural development (mainly sugarcane growing) but contrasting riparian vegetation (intact native rainforest vs. exotic weeds). There were strong gradients in water quality and consistent differences between streams. The most significant pattern was an increase in nitrate+nitrite (NOx) concentration with distance downstream, reflecting the increasing discharge and proportion of fertilized agricultural land in the catchment, and indicating continuous export of contaminated groundwater along all streams. Measuring water quality along the longitudinal gradient was critical to the interpretation of the data and enabled us to confidently detect differences between streams. NOx concentrations and loads were significantly lower in streams with greater riparian vegetation and regression analysis suggested some N-stripping in the riparian zone, albeit insufficient to meet regional water-quality guidelines. Our results demonstrate the benefit of accounting for longitudinal gradients in comparing water quality among streams and in detecting the effect of riparian vegetation at a catchment scale, but that adequate reduction in NOx in streams can only be achieved by reduced fertilizer application rates in the catchments.