Heavy metal (HM) pollution in sediments is tightly related to the security of water quality in rivers, but the accumulation and conversion of HMs are poorly researched, so that a field study was conducted as an example in the Liujiang River Basin. Seven HMs were analyzed to determine between the overlying water and sediments. Moreover, the regulation of HMs speciation and environmental factors in their accumulation and conversion were identified. The obtained results suggested the HM concentrations in water are far below the primary standard of water quality, but in sediments, the contents of Cd and Zn are significantly higher than their corresponding baseline of soil. Only Cd and Pb are dominantly in non-residual form (carbonate-bound fraction and reducible fraction, respectively). The non-significant correlations suggested pH and Eh may be hard to influence HMs in water, while the significant correlations highlighted the regulations of Eh, organic matter and mean grain size on the accumulation of metals in sediments. The opposite correlations between EC, TDS, pH and Cd confirmed the emission of acid wastewater contributed to the accumulation of Cd in sediment. The conversion of metals between water and sediments were found to be significant only in specific forms of Cd, As, Cu, Zn and Pb, suggesting the conversion of HMs in sediments should be largely regulated by their specific forms. The very high risk disclosed by the higher values of Eri and RI are only found upstream, while the higher risk of Cd should be treated as a critical environmental threat.