the likeliest, in my opinion, is a pH imbalance of some sort -- ie, bacterial vaginosis (possibly also a yeast infection, but BV or something called trichomoniasis, which is also a possibility and also easily treated with a round of antibiotics, are the likeliest culprits). BV sounds a lot worse than it really is, and is not necessarily a STI; but it's still in your best interest to go through a round of antibiotics after sexual activity with someone you suspect has BV, because you could pass it on to others.
the other possibility is that... and this one is significantly grosser... that she accidentally left a feminine product (ie a tampon) in there and forgot about it, and now it's lodged pretty deeply inside her vaginal cavity. :-/
yes, there is, of course, a nice way to tell her. that doesn't mean she'll like to hear it... but she needs to hear it. while there is a range of feminine scent (i've been with women who have a very delicate, almost floral sort of scent; and women with a more pungent, earthy/musky scent), a fishy smell is not generally normal. i would just gently advise her that she smelled a bit 'off.' tell her that you enjoyed her time with her, but are sincerely concerned about her health. that won't guarantee she'll be okay with the news, but... it's the more ethical thing, IMO, to tell her. i would want to know.