Intensive agriculture profoundly alters the geomorphology, hydrology and nutrient balances of catchments. The result is the degradation of headwater stream ecosystems via inputs of excess sediments, surface runoff, and nutrients. To mitigate the negative effects on streams, watershed managers can implement riparian buffers, which are designed to intercept, process, store, and remove excess material from upslope agricultural source areas. While extensive research on those topics exists for temperate regions of developed countries, little is known in tropical regions of developing countries. To address this knowledge gap, I investigated the effects of sugarcane agriculture on catchment geomorphology and headwater stream ecosystems in Brazil. I studied 11 first and second order catchments spanning a sugarcane-forest gradient near Piracicaba, SP, to answer three main questions. (1) Is sugarcane agriculture an important agent of geomorphological change via gully formation? (2) Does gully formation influence the effectiveness of riparian buffers while increasing the stream response to storm events, and the amount of sediment in high flows? (3) Can land cover history in terms of sugarcane, and forest cover explain the variability in stream nutrient (nitrogen and phosphorus) concentrations? The overall results suggest that sugarcane agriculture is a driver of geomorphic alteration via gully formation in small order catchments in Brazil. Gullies act as effective conduits of surface runoff from upslope source areas to streams, increasing the magnitude of the stream’s response to storms and the amount of sediment transported in high flows. Consequently, gully formation may overwhelm any protective role played by riparian buffers. Sugarcane agriculture also increases stream nutrient concentrations to a point rarely recorded for streams draining intensive cropping in Brazil. However, there is little evidence that forested riparian buffers significantly mitigates the extent to which sugarcane agriculture affects stream nutrient concentrations. Additional policies to the restoration of riparian forests are needed to effectively protect headwater streams in Brazil.