Land use activities impair stream ecosystems and can result in changes in biodiversity and stream ecosystem function. In streams, benthic biofilm communities can be strongly affected by watershed land use. For example, reduction or removal of riparian vegetation related to land use activities can result in a shift in metabolism towards high primary productivity. We study the response of benthic biofilm function and biodiversity to watershed land use in low-order streams in the Turabo Watershed, Caguas, Puerto Rico. Dominant land use in each subwatershed using aerial images indicated that sites ranged from forested riparian vegetation to mainly surround by pastures and houses. Benthic biofilms biodiversity was determined using molecular techniques (e.g. TRFLP) and metabolism using chambers. Our study shows that benthic biofilm metabolism reflects changes in land use, mainly those related to decreases in riparian vegetation and increases in light availability. Biofilm biodiversity showed a clear change with land use, with reduced diversity of phylotypes in urban streams related to forested streams. Our study shows that changes in biofilm function are the result of changes in the environment and in the diversity.