To study the distribution characteristics of diatom communities in relation to the gradient of water quality and land-use, water samples and epilithic diatoms were collected from 90 sites including mainstream and tributaries, in the Geum River System (GRS) during no rainfall, May 2011. Of 239 taxa identified, Achnanthes convergens and Cymbella minuta were dominated over all the sites. Cluster analysis on the GRS divided into three groups. Group 1 (G1) is the mountainous upstream, a relatively good water quality, and mainly consisted of saproxenous species. Group 2 (G2) is the urban sites, polluted (high in electric conductivity, total phosphate and soluble reactive phosphorus), and saproxenous and common species. Group 3 (G3) is the agriculture sites, and polluted (turbidity, total nitrogen, nitrate), and saprophilous species. There were some discrepancies between abiotic and biotic variables in GRS; biologically similar between G1 and G2, but abiotically similar between G2 and G3. These differences may attribute to not only physiological characteristics of diatom cells, but complicate relationships between microhabitat and water quality. Thus, an urgent development of generalized or standardized methods to diminish the differences between epilithic diatom community and environments is advent.