Sediments were collected from the upper, middle and lower reaches of both urban and rural rivers in a typical urbanization zone of the Pearl River delta. Six heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) were analyzed in all sediment samples, and their spatial distribution, pollution levels, toxicity and ecological risk levels were evaluated to compare the characteristics of heavy metal pollution between the two rivers. Our results indicated that the total contents of the six metals in all samples exceeded the soil background value in Guangdong province. Based on the soil quality thresholds of the China SEPA, Cd levels at all sites exceeded class III criteria, and other metals exhibited pollution levels exceeding class II or III criteria at both river sites. According to the sediment quality guidelines of the US EPA, all samples were moderately to heavily polluted by Cr, Cu, Ni, Pb and Zn. Compared to rural river sites, urban river sites exhibited heavier pollution. Almost all sediment samples from both rivers exhibited moderate to serious toxicity to the environment, with higher contributions from Cr and Ni. A "hot area" of heavy metal pollution being observed in the upper and middle reaches of the urban river area, whereas a "hot spot" was identified at a specific site in the middle reach of the rural river. Contrary metal distribution patterns were also observed along typical sediment profiles from urban and rural rivers. However, the potential ecological risk indices of rural river sediments in this study were equal to those of urban river sediments, implying that the ecological health issues of the rivers in the undeveloped rural area should also be addressed. Sediment organic matter and grain size might be important factors influencing the distribution profiles of these heavy metals.