The pressures of a growing population and a fluctuating economy have caused extensive landuse transformations in the Colombian Andes, and >63% of the natural land cover has been replaced by cattle and crop fields. Despite the obvious importance of agriculture as a driver of stream degradation, the specific effects of agriculture on low-order streams of the Andean region are poorly understood. We used aquatic macroinvertebrates as indicators of biological integrity and applied structural equation modeling (SEM) to explore mechanisms through which local agricultural practices degrade headwater streams of the Colombian coffee-growing region. Our results suggest that agriculture affects the aquatic macroinvertebrate community indirectly by increasing the concentration of NH3-N in the water and reducing the width of the riparian forest. Moreover, through the reduction of riparian forest width, agriculture increased % slow-flowing habitats and decreased the availability of coarse substrates in the reach, which also had important effects on the benthic community. These results indicate that local farming practices, such as the elimination of the riparian forest and the use of riparian zones for crops and cattle grazing, are responsible for most of the effects of agriculture on streams in this region. Our results also highlight the importance of further research to formulate management alternatives relevant to the local context.