In southern Taiwan, almost all the main rivers have been contaminated by anthropogenic heavy metals and organic matters. The main pollution sources include agricultural, industrial, and domestic activities. River sediments potentially have large capacities to accumulate heavy metals and organic matters when the river water flows through it. The sediments sampled from high contaminated river (the Yenshui River) and moderately contaminated rivers (the Tsengwen, Chishui, Potzu, and Peikang Rivers) were used to realize correlations between each kind of aqua regia extractable heavy metals (Co, Cr, Cu, Zn, Ni, Pb, Mn, and Fe) and organic matters in vertical sediment cores. Organic matters and aqua regia extractable heavy metal concentrations, analyzed by strong acid-digested extraction, were determined in vertical profile segments from downstream sediments of the five rivers. Sum of six aqua regia extractable heavy metals (Co, Cr, Cu, Zn, Ni, and Pb) were below 3,000 mg/kg in sediments of the Yenshui River, and below 500 mg/kg in the other four rivers' sediments. Strongly positive correlations (r = 0.83-0.95) between each kind of aqua regia extractable heavy metals and organic matters (concentration range between 0.6 to 3.8%) were observed in sediments of the Yenshui River. The slopes of the linear regressive lines approximated the average metal complexation ratios with organic matters in the sediments. In sediments of the other four rivers, smaller positive correlation coefficients between aqua regia extractable heavy metals and organic matters (below 2.6%) were observed. The complexation ratios derived from the four moderately polluted river sediments were smaller than those derived from the highly contaminated river sediments, indicating that the importance of organic matters in the accumulation of heavy metals in river sediments.