The presence of pharmaceuticals in nature systems poses a threat to the environment, plants, animals, and, last but not least, human health. Their transport in soils, waters, and sediments plays important roles in the toxicity and bioavailability of pharmaceuticals. The mobility of pharmaceuticals can be affected by their interactions with organic matter and other soil and water constituents. In this study, a model agarose hydrogel enriched by humic acid as a representative of organic matter is used as a transport medium for pharmaceuticals. Sulphapyridine (as a representative of sulphonamide antibiotics) and diclofenac (as a representative of widely used non-steroidal anti-inflammatory drugs) were chosen for experiments in diffusion cells. Pharmaceuticals were passed through the hydrogel from the donor solution to the acceptor compartment and could interact with humic acids incorporated in the hydrogel. The lag time was prolonged if the hydrogel was enriched by humic acids from 134 to 390 s for sulphapyridine and from 323 to 606 s for diclofenac. Similarly, the incorporation of humic acids in the hydrogel resulted in a decrease in the determined diffusion coefficients. The decrease was stronger in the first stage of the experiment when diffusing particles could interact with vacant binding sites.