Glycosaminoglycans (GAGs), such as hyaluronic acid (HA) and chondroitin sulfate (CS), have seen widespread adoption as components of tissue engineering scaffolds because of their potent bioactive properties and ease of chemical modification. However, modification of the biopolymers will impair biological recognition of the GAG and reduce the bioactive properties of the material. In this work, we studied how the degree of thiolation of HA and CS, along with other key hydrogel design parameters, affected the physical and bioactive properties of the bulk hydrogel. Although properties, such as the HA molecular weight, did not have a major effect, increasing the degree of thiolation of both HA and CS decreased their biorecognition in experimental analogues for cell/matrix remodeling and binding. Furthermore, combining HA and CS into dual polymer network hydrogels also modulated the physical and bioactive properties, as seen with differences in gel stiffness, degradation rate, and encapsulated cell viability.