Melanins are biopolymers encompassing a high degree of chemical heterogeneity. Binding of small-molecule drugs to ocular melanin significantly affects the ocular pharmacokinetics, and could serve as a strategy for prolonged drug retention in the eye. The influence of the structural and physical characteristics of melanins originating from different sources on their drug binding properties has not yet been methodically investigated. We performed physical characterization of Sepia officinalis, synthetic and porcine melanin. The particle size distribution was analyzed by laser diffractometry. A dynamic vapor sorption method, requiring small amounts of the material, was developed to analyze the differences in the specific surface area of the melanins. The extent of melanin binding at equilibrium was determined for a set of 34 small-molecule drugs and compared across different melanin types. Despite systematic shifts in the extent of binding within a twofold range, binding data were highly correlated across the melanins. These moderate differences in binding could not be directly explained by the substantial differences in particle size and were more in line with the relatively similar specific surface area of these different melanin materials. Overall, these results suggest that the specific surface area reflects the actual accessibility of a small molecule in the melanin structure and could serve as a surrogate to explain the binding differences observed for the respective melanin materials.