A Serratia sp. bacterium manufactures amorphous calcium phosphate nanominerals (BHAP); this material has shown increased sorption capacity for divalent radionuclide capture. When heat-treated (≥450 °C) the cell biomass is removed and the biominerals are transformed to hydroxyapatite (HAP). Using a multimethod approach, we have elucidated both the site preferences and stability of analogue radionuclide incorporation for Sr, Co, Eu, and U. Strontium incorporates within the bulk amorphous inorganic phase of BHAP; however, once temperature modified to crystalline HAP, bonding was consistent with Sr substitution at the Ca(1) and/or Ca(2) sites. Cobalt incorporation occurs within the bulk inorganic amorphous phase of BHAP and within the amorphous grain boundaries of HAP. Europium (an analogue for trivalent actinides) substituted at the Ca(2) and/or the Ca(3) position of tricalcium phosphate, a known component of HAP grain boundaries. Uranium was surface complexed with no secondary minerals detected. With multiple sites for targeted radionuclide incorporation, high loadings, and good stability against remobilization, BHAP is shown to be a potential material for the remediation of aqueous radionuclide in groundwater.