Anthropogenic land use within watersheds has substantial effects on aquatic habitats and biological communities. From September 2006 to December 2008, we investigated the effects of land use on benthic macroinvertebrate communities by comparing Song Stream and Odae Stream, two adjacent mountain streams in Korea whose watersheds have different land use patterns. Song Stream is significantly disturbed by agricultural activities in the watershed, whereas Odae Stream is relatively undisturbed and is surrounded by a well-conserved forest area. Song Stream had significantly higher levels of all nutrients and sediment-related factors due to the adjacent agricultural area. As a result, Song Stream had markedly lower species community indices, such as taxa richness and abundance. In Song Stream, macroinvertebrate scrapers and predators were most adversely affected, whereas collector-gatherers became a dominant group. Based on correlation and multivariate analyses, total dissolved solids had the strongest negative relationship with macroinvertebrate assemblages, followed by electrical conductivity, total nitrogen, and pH. The proportion of cobble in stream substrate was positively related to the richness and abundance of macroinvertebrates. Our results indicate that disturbances caused by agricultural land use, particularly sand deposition, had significant adverse effects on macroinvertebrate habitats and on the biotic integrity of benthic macroinvertebrate communities.