The success of stabilization treatment in heavy metal contaminated sediment depends on the heavy metal bioavailability reduction through the sequestration of the heavy metals. This study was performed to assess the changes in the bioavailability of Pb or Cd in the Pb or Cd contaminated sediments by using birnessite and hydroxyapatite as stabilizing agents. The toxicity tests were carried out using a microorganism (Vibrio fischeri), an amphipod (Hyalella azteca) and an earthworm (Eisenia foetida). With Vibrio fischeri, the toxicities of both Pb and Cd were reduced by more than ten times in the presence of birnessite and hydroxyapatite compared to that of in the absence of birnessite and hydroxyapatite. The concentrations of Pb and Cd in the contaminated sediments were lethal to Hyalella azteca, however, in the presence of birnessite and hydroxyapatite more than 90%, on average, of Hyalella azteca survived. With Eisenia foetida, the bioaccumulated concentrations of both Pb and Cd were reduced by more than 75%, on average, lower with the addition of birnessite and hydroxyapatite to the contaminated sediments. These results show that the addition of birnessite and hydroxyapatite can reduce the bioavailability of Pb and Cd in contaminated sediments. In addition, the in situ and ex situ performance of birnessite and hydroxyapatite as stabilizing agents can be verified using the toxicity tests with Hyalella azteca and Eisenia foetida, respectively.