Stopping powers of antiprotons in H2 and H2O targets are calculated using a semiclassical timedependent convergent close-coupling method. In our approach the H2 target is treated using a twocenter molecular multiconfiguration approximation, which fully accounts for the electron-electron correlation. Double ionization and dissociative ionization channels are taken into account using an independent-event model. The vibrational excitation and nuclear scattering contributions are also included. The H2O target is treated using a neonization method proposed by Montanari and Miraglia [J. Phys. B 47 015201 (2014)], whereby the ten-electron water molecule is described as a dressed Ne-like atom in a pseudo-spherical potential. Despite being the most comprehensive approach to date, the results obtained for H2 only qualitatively agree with the available experimental measurements.