We determine the index of five of the seven hypergeometric Calabi–Yau operators that have finite index in $\mathit{Sp}_{4}(\mathbb{Z})$ and in two cases give a complete description of the monodromy group. Furthermore, we find six nonhypergeometric Calabi–Yau operators with finite index in $\mathit{Sp}_{4}(\mathbb{Z})$, most notably a case where the index is one.