Glycosaminoglycans (GAGs) are a class of linear polysaccharides that are ubiquitous in the extracellular matrix (ECM) and on cell surfaces. Due to their key role in development, homeostasis, pathogenesis, and regeneration, GAGs are increasingly used in the design of ECM-mimicking hydrogels to stimulate tissue formation and regenerative processes via specifically orchestrated cell-instructive signals. These applications first and foremost build on the ability of GAGs to effectively bind, protect, and release morphogens. The specificity and strength of morphogen-GAG interactions are largely governed by the number and spatial distribution of negatively charged sulfate groups carried by GAGs. Herein, we summarize a mean-field approach to quantify the density of ionizable groups, GAG concentration, and cross-linking degree of GAG-containing hydrogels on the basis of microslit electrokinetic experiments. We further present and discuss a continuum model of mucosa that accounts for charge regulation by glycan-ion pairing in biological contexts and under conditions of macromolecular crowding. Finally, we discuss the modulation of the morphogen binding and transport in GAG hydrogels by selective desulfation of the GAG component.