Molecules that get charged in Water
It depends on the context how he meant it. I could imagine two scenarios:


Certain materials can produce ions when they dissolved in water. A typical example is table salt, NaCl. Table salt is solid form has a lattice that contains Na+ and Cl+ ions, and when you put it in water, the water molecules can help releasing these ions into the solution, where you now can find the ions. Note, that in this case the ions are atomic entities but molecules with charge are also ions, like $\ce{MnO4-}$ or $\ce{SO}_4^{2-}$. 
Another scenario when the charged entities are formed as a reaction with water by e.g. giving an electron (oxidation) to water molecules or to other dissolved components e.g. oxygen in water. As you can imagine, it happens generally with very reactive materials (materials that are very sensitive to moisture), but essentially the rusting of iron is a similar reaction.