Surface charge states of biomaterials are often important for the adsorption of cells, proteins, and foreign ions on their surfaces, which should be clarified at the atomic and electronic levels. First-principles calculations were performed to reveal thermodynamically stable surface atomic structures and their charge states in hydroxyapatite (HAp). Effects of aqueous environments on the surface stability were considered using an implicit solvation model. It was found that in an air atmosphere, stoichiometric {0001} and P-rich {100} surfaces are energetically favorable, whereas in an aqueous solution, a Ca-rich {100} surface is the most stable. This difference suggests that preferential surface structures strongly depend on chemical environments with and without aqueous solutions. Their surface potentials at zero charge were calculated to obtain the isoelectric points (pH_PZC). pH_PZC values for the {0001} surface and the Ca-rich {100} surface were obtained to be 4.8 and 8.7, respectively. This indicates that in an aqueous solution at neutral pH, the {0001} and Ca-rich {100} surfaces are negatively and positively charged, respectively. This trend agrees with experimental data from chromatography and zeta potential measurements. Our methodology based on first-principles calculations enables determining macroscopic charge states of HAp surfaces from atomic and electronic levels.