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Alginate is a naturally occurring polysaccharide that consists of guluronic and mannuronic acid residues. Although it has been widely exploited in drug delivery because of its favorable properties (biocompatibility, ease of processing, and gelling capability under mild conditions), most alginate-based systems show poor sustained-release drug release because of the high erosion rate of alginate-based hydrogels. This study exploited the effect of three inorganic nanoparticulate modifiers (including montmorillonite clay material, silver nanoparticles, and iron-based magnetic nanoparticles) on the encapsulation and controlled release of favipiravir, which served as a model for poorly soluble drugs. Structures of the generated nanoparticles were characterized by using UV–visible spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), and thermogravimetric analysis (TGA) to examine interactions between the loaded drug and the components of the nanoparticles. The incorporation of various nanoparticulate modifiers into alginate-based nanoparticles had little effect on the drug release mechanism, with all modified nanoparticles following a Super Case-II transport mechanism in which the drug release rate was governed by the relaxation of the polymeric chains. However, nanoparticles incorporated with different modifiers show variations in porosity and hydrophilicity. This caused ultimate changes in drug encapsulation efficiency and release sustainability.