Millimetric spherical beads of a biocompatible composite were produced from sodium alginate, a natural polysaccharide, and nanostructured hydroxyapatite (HA). It was shown that the composite was effective in the removal of lead ions and lead phosphate nanoparticles from high-contaminated simulated gastric fluid. X-ray diffraction spectroscopy and scanning electron microscopy analyses performed on HA–alginate beads after the Pb2+ uptake showed that nanocrystals of a lead phosphate, [Pb10–xCax(PO4)6Cl2], were precipitated on the bead surface. The cross-linked polymer chain had a double role: (i) keep Pb2+ ions and lead phosphate nanoparticles bounded to the bead surface, preventing their bioavailability in stomach fluid; and (ii) delay HA dissolution in the acidic conditions of the stomach, assuring that an excess of Ca2+ will not be released to simulated gastric fluid. Desorption experiments in simulated enteric fluid revealed that lead remained immobilized in the calcium phosphate phase in the intestinal tract. These results indicate HA–alginate composite as a potential system for heavy metals removal from contaminated gastric and enteric human fluids, minimizing its adsorption by the human body.