Be careful how you label your species here. OH- can be seen as a base (and a nucleophile) but H2O is not the conjugate acid in the sense that you mean, H3O+ would be the 'acid'. This is because (using your HCl equation) HCl does not simply become two separate ions in solution. The acid will protonate H2O to become H3O+.
But remember, all these reactions are in equilibrium and the pKa determines to what extent the different species exist.