Hydrogels are used in drug delivery applications, chromatography, and tissue engineering to control the rate of solute transport based on solute size and hydrogel-solute affinity. Ongoing modeling efforts to quantify the relationship between hydrogel properties, solute properties, and solute transport contribute toward an increasingly efficient hydrogel design process and provide fundamental insight into the mechanisms relating hydrogel structure and function. However, here we clarify previous conclusions regarding the use of mesh size in hydrogel transport models. We use 3D geometry and hydrogel network visualizations to show that mesh size and junction functionality both contribute to the mesh radius, which determines whether a solute can diffuse within a hydrogel. Using mesh radius instead of mesh size to model solute transport in hydrogels will correct junction functionality-dependent modeling errors, improving hydrogel design predictions and clarifying mechanisms of solute transport in hydrogels.