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We don't know what he whispered to her in "Let's Kill Hitler" but, from her reply, "I'm sure she knows," it was probably something like, "Tell River I love her."

We do know what he whispered to her in "The Wedding of River Song", because she told Amy at the end of the episode that he'd told her to look into his eye & when she did so she saw the miniaturised Doctor inside what she then realised was the Teselecta.