It has been two years since my son, daughter and I went. However, we quite enjoyed it. It certainly does not take all day and I'd almost lay wager that a three-year-old's attention span would wane within a couple of hours anyway.
If she's a young three, you may be able to take her in for free, otherwise, prices apply.
There are two-for-one tickets available if you're travelling via National Rail. The same applies for the London Eye. If she's still awake after all of this, you might 'finish her off' with a saunter over to the London Transport Museum at Covent Garden. It's far more interactive for a small person. Yet when I did this, my daughter preferred the aquarium and my son preferred the museum. - Go Figure!
Book in advance, on-line, to get the best offer if you're not using any discount codes, etc.
http://www.daysoutguide.co.uk/london-aquarium
Bon Journey!
Have a great trip!