Aquasomes form a three-layered structure, made of a polyhydroxy oligomer coated core upon which the drug is loaded. The biochemically active molecules are able to interact with the coated core through different Van der Waal forces, entropic forces, and ionic and non-covalent bonds. The structure of aquasomes enables them to carry a variety of substrates, facilitating applications such as protein and peptide delivery and protection, and the delivery of nucleic acids for gene therapy applications. The tri-layer formulation is attributed to several drug delivery properties of the aquasome. 
Aquasomes’ solid core, made of ceramic or polymeric material, is attributed to the structural stability of the nanoparticle itself, and can result in improved solubility and biocompatibility of the drug. Different core designs have also been shown to affect the controlled release properties of the drug molecule. A commonly used core material is the ceramic calcium phosphate, which naturally occurs in the body. Hydroxyapatite, which is found in bone, is another commonly used core material. Hydroxyapatite cores have been shown to contribute to targeted delivery of encapsulated hepatitis B antigens intracellularly. However, the ability to target aquasomes to specific cells or tissues has not been explored beyond intracellular delivery of aquasome payloads.
The second layer of aquasomes is the carbohydrate coat, onto which the drug is adsorbed. Due to carbohydrate’s action as a dehydroprotectant, it has been shown to function as a natural stabilizer to preserve the conformation and shape of soft drugs. The dehydroprotectant property of the carbohydrate coat also enables protection of the biochemically active molecule from dehydration and protein degradation.
The size of aquasomes ranges from 60 to 300 nanometers, hence their characterization as a nanoparticle drug carrier. The nanoscale of aquasomes gives them a high surface area to volume ratio. The smaller the core, the higher the surface area to volume ratio, which increases the drug loading capacity of the aquasome. Aquasomes possess water-like properties due to the presence of the carbohydrate coating, enabling them to protect and preserve fragile biological molecules. The size of aquasome particles increases as a function of the ratio between the concentration of the core to the coat due to the availability of free surface core particles for the coating material.
The self-assembly process of aquasomes into their tri-layer structure is achieved by non-covalent and ionic bonds, along with physicochemical properties of their components. Calcium phosphate nanoparticles are formed before the carbohydrate coat is adsorbed onto the surface of the core through electrostatic interactions. Layers are then added to the structure to achieve desired size, while crosslinked polymers aid in further stabilization. The sonication process during the reaction of disodium hydrogen phosphate and calcium chloride to prepare calcium phosphate impacts the self-assembly process of aquasomes by increasing surface free energy of the core prepared. This assembly process allows the design of aquasomes for specific drug delivery applications.
The structure of aquasomes can contribute to controlled drug release, drug stability, and intracellular targeting of the drug. Other commonly used nanoparticle drug delivery systems include niosomes, liposomes, and vesosomes, the compositions of which contribute to different properties of the resulting nanoparticle compared to aquasomes. Niosomes are composed of non-ionic surfactants and bilayer structures, allowing them to encapsulate hydrophilic and hydrophobic drugs. Liposomes are composed of phospholipids and a similar bilayer structure to niosomes, and can deliver toxic or poorly soluble drugs. Vesosomes have a core-shell structure similar to aquasomes, but contain a lipid bilayer core and a polymer shell, while aquasomes consist of a ceramic or polymeric core and a carbohydrate coat. Vesosomes are used for encapsulating imaging agents and aiding in imaging techniques such as MRI.