Hydrogels are widely used materials which have many medical applications. Their ability to absorb aqueous solutions and biological fluids gives them innovative characterizations resulting in increased compatibility with biological activity. In this sense, they are used extensively for encapsulation of several targets such as biomolecules, viruses, bacteria, and mammalian cells. Indeed, many methods have been published which are used in hydrogel formulation and biomedical encapsulations involving several cross-linkers. This system is still rich with the potential of undiscovered features. The physicochemical properties of polymers, distinguished by their interactions with biological systems into mucoadhesive, gastro-adhesive, and stimuli responsive polymers. Hydrogel systems may be assembled as tablets, patches, gels, ointments, and films. Their potential to be co-formulated as nanoparticles extends the limits of their assembly and application. In this review, mucoadhesive nanoparticles and their importance for biomedical applications are highlighted with a focus on mechanisms of overcoming mucosal resistance.