The effect of the topological structure; that is, the network heterogeneity, of hydrophobically modified, slightly acidic hydrogels on the binding and release of low molar mass drugs has been studied using ibuprofen and ephedrine as model compounds with varying water solubility. The difference in the heterogeneity of the gels has been produced by the choice of the hydrophobe copolymerized into the polymer network. The effect of the drug loading on the release kinetics has been investigated as well. The release of hydrophobic ibuprofen was slower from a strongly aggregated heterogeneous gel than from a more homogeneous one, because of the strong hydrophobic interaction between ibuprofen and the heterogeneous hydrogel. The release of hydrophilic ephedrine from the homogeneous gel with an initial drug content of 30 wt % of dry polymer showed negative time dependence, indicating that during and after the swelling of the gel, ephedrine started to bind to the polymer. However, the release of ephedrine from a heterogeneous hydrogel increased with time. This shows that the heterogeneous, aggregated polymer binds the hydrophobic substance more strongly than the homogeneous one does, and that the homogeneous network has higher affinity for the basic hydrophilic substance than the heterogeneous one does. The loading contents of ibuprofen and ephedrine affect the release rates in different ways because of the different binding and release mechanisms. The number of binding sites accessible for ephedrine inside the polymer network is assumed to change upon the swelling of the gel.