The Atoms in Molecules Theory description for the X-O (X=N,P) bonds in hypervalent molecules has been tested at various levels and basis sets. Calculations in H₃PO, F₃PO, H₃NO, F₃NO molecules have been carried out at the HF, B3LYP and MP2(full) levels using the 3-21G, 3-21G*, 6-31G, 6-31G*, 6-311G, 6-311+G* and 6-311+G(3d,2p) basis sets, showing that polarization functions are essential for an adequate geometrical description of hypervalent molecules, especially when second row atoms are present. The dependence of the numerical parameters at the different bond critical points and the Bader charges on X and O atoms have been studied by the aforementioned methods. The AIM analysis is independent from the chosen level or basis sets, when polarization function are present. The geometry dependence of the X-O Bader analysis has also been tested by performing calculations for H₃PO by varying P-O bond lengths. This analysis has been proven as invariable for medium bond lengths variations. The results are also compared with the H₃P···O van der Waals complex.