An imbalance between tissue-degrading matrix metalloproteinases (MMPs) and their counterparts' tissue inhibitors of metalloproteinases (TIMPs) causes pathologic extracellular matrix (ECM) degradation in chronic wounds and requires new adaptive biomaterials that interact with these regulators to re-establish their balance. Sulfated glycosaminoglycans (GAGs) and TIMP-3 are key modulators of tissue formation and remodeling. However, little is known about their molecular interplay. GAG/TIMP-3 interactions were characterized combining surface plasmon resonance, ELISA, molecular modeling and hydrogen/deuterium exchange mass spectrometry. We demonstrate the potential of solute and surface-bound sulfated hyaluronan (sHA) and chondroitin sulfate (sCS) derivatives to manipulate GAG/TIMP-3 interactions by varying GAG concentration, sulfation degree and chain length. Three GAG binding sites in the N- and C-terminal domains of TIMP-3 were identified. We reveal no overlap with the matrix metalloproteinases (MMP)-binding site, elucidating why GAGs did not change MMP-1/-2 inhibition by TIMP-3 in enzyme kinetics. Since we prove that GAGs alone have a low impact on MMP activity, sHA and sCS offer a promising strategy to possibly control ECM remodeling via stabilizing and accumulating TIMP-3 by maintaining its MMP inhibitory activity under GAG-bound conditions. Whether GAG-based functional biomaterials can be applied to foster chronic wound healing by shifting the MMP/TIMP balance to a healing promoting state needs to be evaluated in vivo. Increased levels of tissue-degrading matrix metalloproteinases (MMPs) lead to pathologic matrix degradation in chronic wounds. Therefor functional biomaterials that restore the balance between MMPs and tissue inhibitors of metalloproteinases (TIMPs) are required to promote wound healing. Since sulfated glycosaminoglycan (GAG) derivatives demonstrated already to be e.g. anti-inflammatory and immunomodulatory, and native GAGs interact with TIMP-3 the former are promising candidates for functionalizing biomaterials. We identified the GAG binding sites of TIMP-3 by combining experimental and molecular modeling approaches and revealed that GAG derivatives have a higher capacity to sequester TIMP-3 than native GAGs without altering its inhibitory potential towards MMPs. Thus GAG derivative-containing biomaterials could protect tissue from excessive proteolytic degradation e.g. in chronic wounds by re-establishing the MMP/TIMP balance.