The bioavailable contents of heavy metals in karstic soils are a subject of increasing concern since the uptake of heavy metals by plants can pose a severe threat to food safety and public health. However, the bioavailable contents of heavy metals and their effective factors are poorly understood in karst regions. Calcareous soil and red soil developed from carbonate and clastic rocks, respectively, were chosen from a typical karst region (Guilin) of southwestern China, and the total (CT) and available (CA) contents of 11 heavy metals, as well as their influencing factors in soil profiles, were investigated. The results showed that calcareous soil has greater soil organic carbon, total nitrogen, available nitrogen, available potassium, and calcium (Ca) contents than red soil, but lower available phosphorus and C:N. Acid-soluble Ca (Aca) was the dominant fraction in both types of soil. Heavy metals were highly accumulated in calcareous soil, mainly controlled by secondary enrichment in the processing of carbonate rock weathering. For the majority of metals, calcareous soil had higher CT and lower CA than red soil. According to a redundancy analysis (RDA) and Pearson correlation coefficient, the high pH and Ca content in calcareous soils were primary factors influencing both the CT and CA of the metals, especially residual Ca to CT and Aca to CA. Additionally, higher soil cation exchange capacity and clay minerals also probably improved the immobility of heavy metals.