The aim of this work is to elucidate the structure of the new hydrogel prepared with scleroglucan (Sclg) and borax, suitable for drug delivery, applying theoretical approaches, and to explain its very peculiar swelling. The possible linkages with borate ions have been investigated and original parameters for the 4,6-gluco-borate moiety have been introduced. The structures relative to the Sclg chains in the presence of borax and the possible mutual arrangements among the triple helices are given. According to molecular dynamics simulations, the most probable assembly of the chains in the network is proposed, without and in the presence of three tested model drugs with different molecular dimensions: theophylline (TPH), Vitamin B12 (Vit. B12) and myoglobin (MGB). The hydrogel supramolecular structure, formed via chemical and physical linkages among the polysaccharidic chains, is built up taking into account the steric hindrance of the entrapped molecules. It is shown that molecular dynamics analysis can be a useful tool capable to shed some light on the anomalous swelling of the hydrogel, suitable for drug release, giving a new insight on the network structure and the release rate of the guest molecules.