The presence of large quantities of ZrO2 in certain high-level nuclear waste streams presents a significant problem due to the relatively low solubility of ZrO2 in oxide glasses. Here, molecular dynamic modeling was used to give insights into the structure of two sodium–lithium borosilicate glasses with additions of ZrO2. The structural environment of Zr within the molecular dynamics (MD)-simulated glasses correlated well with that shown in the literature. There has been limited study previously into the changes in bulk glass structure with ZrO2 additions. This work shows that addition of ZrO2 changes the coordination of boron and the polymerization of the glass network due to the requirement for 1 mol of alkali oxide for charge compensation. The change in boron coordination is shown to be nonlinear with the addition of ZrO2. We have also shown a possible method of predicting the solubility limits of oxides within glasses from MD simulations.