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Streams are usually susceptible to land-use change, mainly in the tropics due to high dynamic climatic conditions. Native forests have been converted for agricultural purposes with significantly impacts in streams. Nowadays, forests plantations are taking place of some degraded land and its influence in headwater streams are not well understood in tropical high-allude streams. Thus, this study aims to assess effects of land-use changes from pasture to Eucalyptus plantations in Colombian Andean catchments on stream water conditions and structural characteristics of stream channels. The study was conducted in three catchments, one catchment covered by pasture, one catchment that was converted from pasture to Eucalyptus plantations in 1995 and one pristine catchment with native forest cover. Physical, chemical and biological conditions of stream water were assessed by measurements of water temperature, concentration of dissolved oxygen and chlorophyll-a content of epiphytic communities. The structural characteristics of stream channels were evaluated using a visual-based habitat assessment protocol from the United States Environmental Protection Agency. Principal Component Analysis (PCA) showed native forest and Eucalyptus plantations catchments associated with stream conservation characteristics and pasture catchment with overall degraded conditions. However, the Permutational multivariate analysis of variance (PERMANOVA) showed significant differences between all streams indicating that, despite the overall positive conservation aspects of native and Eucalyptus catchments, their still different from each other. Pasture catchment showed the highest values for temperature and chlorophyll-a, and the lowest values for dissolved oxygen and final score for structural characteristics. Therefore, our results demonstrated that the land-use change from pasture to Eucalyptus plantation improved the stream water conditions and the structural characteristics of the studied headwater streams. Additionally, we propose the use of the rapid bioassessment protocol coupled some stream water characteristics as a rapid and useful tool for detecting effects of land-use changes on high-altitude Andean streams.