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A strange man in "The Library" where the people inside it have disappeared for unexplained reasons, she probably thought, "that must be him, but...why does he look different?"
This could also be explained by the fact that the Doctor may have taught her a method of recognizing him other than by his face, as the Daleks also seem capable of. Or she may have seen footage of his former regenerations while journeying with him in the TARDIS. There is also a length of time between the events "The Waters of Mars" and his regeneration into the Eleventh Doctor that we haven't seen. The Doctor very may well have spent some time with River Song then. In short, there's numerous ways River Song could have seen the Doctor's Tenth form.
I recently read that River is a time traveler, and when she needs to, can go to a point in time to mett any of the Doctor's previous incarnations. In short, she has probably met all 11 Doctorors, maybe even beyond that.
Also, in the 4th episode of Doctor Who series 5, with the new Doctor (Matt Smith), professor River Song is in the episode, by Adam Comer
In Time of the Angels (the 4th episode of series 5), a younger Dr. River Song (not yet Professor) tells the 11th Doctor that she has pictures of all of his incarnations. So, the later River Song who meets the earlier Doctor earlier (doesn't time travel make writing fun?) would still have those pictures.
EDIT: River Song in the episode "The Time of the Angels" says she has pictures of all his incarnations, and since it's established in the beginning-ish that she's not a professor, but in the Tenth Doctor episode "Silence In the Library" she is a professor, she must be a time traveler herself, and still have those pictures.link title
FURTHER EDIT: The first form that River saw (in her time stream) was the eleventh doctor in "Let's Kill Hitler" right after she regenerated from Mel's to River.