The bioavailability of heavy metals (HMs) in sediments is closely related to the security of the aquatic environment, but their impacts are poorly researched, particularly in karstic rivers. Therefore, Liujiang River Basin was taken as an example in this study. Seven HMs were analyzed to determine the bioavailability and speciations of HMs in sediments. Moreover, the impacts of environmental factors on HMs were identified. The obtained results suggested that HMs in the sediments are all within their permissible exposure limit (PEL), but Cd and Zn are significantly higher than the soil baseline. Most HMs were found to be in a residual fraction, while their exchangeable fraction was found to be in an extremely low ratio. HMs in bioavailable parts are significantly higher than in the exchangeable and carbonate-bound phases but lower than in the non-residual phase, which demonstrated that HM bioavailability is not confined to the exchangeable and carbonate-bound phases. The correlation coefficients commonly decreased with decreasing speciation ratios, which suggested that the overall bioavailability of metals should be determined by speciation ratios instead of speciations themselves. Noteworthily, most HMs in the residual form were found to be significantly correlated with their overall bioavailability, which highlighted the potential bioavailability of residual form. The non-correlations between pH, electrical conductivity (EC), total dissolved solids (TDS), and HM bioavailability suggested that HMs in the carbonate-bound phase are stable and unsusceptible to environmental variations, while the significant correlations between redox potential (Eh), turbidity, organic matter (OM), main grain size (Mz), and HM bioavailability suggested that HMs in the reducible and oxidizable forms are susceptible to environmental fluctuations. Therefore, the variation of HM bioavailability in karstic rivers is largely regulated by their reducible and oxidizable forms instead of their carbonate-bound form.