Surface sediments from Beiyun River located in the rapidly urbanized Beijing metropolis were collected and analyzed for heavy metals (As, Cd, Cr, Cu, Mn, Ni, Pb, and Zn) to investigate their spatial distribution pattern, ecotoxicology and source identification. Results indicated the average heavy metal concentrations of Cd, Cr, Cu, Pb, and Zn were approximately 4, 2, 3, 2, and 4 times higher than their background values. Spatially, we found the concentrations of heavy metals made significant change in four sections along urbanized river gradients. The contents in midstream of urban region and farmland region (section 2 and section 3) were greater than those in upstream (section 1) and downstream (section 4). However, one-way analysis of variance for spatial analysis suggested there were no significant differences between mainstream and tributaries. The geo-accumulation index (I geo) used to assess the sediment quality exhibited there was a decreasing order for the average I geo of measured heavy metals: Zn (0.82) > Cd (0.53) > Cu (0.50) > Cr (- 0.08) > Pb (- 0.45) > Ni (- 0.96) > Mn (- 0.97) > As (- 1.01), whereas they had different "high-low" orders at different sampling transects. Ecological risk index values showed that section 2 and section 3 revealed a high and moderate ecological risk, respectively. Furthermore, principal component analysis indicated the first principle component explained 64.73% of total variance with the main pollutants of As, Cr, Ni, Zn, and Cu which were probably controlled by the mixed sources covering natural factors and anthropogenic input.