In drug development, it is extremely important to evaluate the solubility and stability of solid states and to immediately determine the potential for development. Salt screening is a standard and useful method for obtaining drug candidates with good solid state properties. Ondansetron is marketed as a hydrochloride dihydrate, and its dehydration behavior was previously reported to transition to an anhydrate via a hemihydrate as an intermediate by heating. Here, we synthesized ondansetron hydrobromide and hydroiodide and examined their dehydration behaviors. Single-crystal structure analysis confirmed that like ondansetron hydrochloride, ondansetron hydrobromide formed a dihydrate. Moreover, the crystal lattice parameters and hydrogen bonding networks were similar and isomorphic. While single-crystal structure analysis showed that ondansetron hydroiodide also formed a dihydrate, the crystal lattice parameters and hydrogen bonding networks were different to those of ondansetron hydrobromide and hydrochloride. Additionally, the dehydration behavior of ondansetron hydrobromide differed from that of the hydrochloride, with no hemihydrate intermediate forming from the hydrobromide, despite similar anhydrate structures. Given that it is difficult to predict how a crystal structure will form and the resulting physical properties, a large amount of data is needed for the rational design of salt optimization.