Possibly a combination of not showing herself much, fiddling when she did, and people not conceiving she could have another child.
On "The 100 writers room" Tumblr (which is official), people asked about birth control on the Ark, and the reply is that every woman has a contraceptive implant, which Aurora got removed "somehow". The writers themselves seem to admit to a bit of handwaving until they "establish" something.
We get this question A LOT as everyone seems really curious about the Ark views on contraception and multiple births.
We’ve established (as has the book on which the show is based) that the Ark maintained strict population controls. Families were allowed one child (by which those births were planned by removing birth control implants to allow conception and then re-implanting the birth control after the baby is born).
In the case of Octavia, her mother had her birth control removed surreptitiously, (or never had it re-implanted after Bellamy was born. We haven’t established this definitively) thus allowing her to give birth to a second child, which she needed to keep hidden below the floor so as to evade discovery…which, ultimately, failed when Octavia was discovered and imprisoned.
As for the "hiding" part, as a comment notices, isolation will most likely be respected on the Ark, for health measures; and when she absolutely needed to show herself, if no one expects her to be pregnant, a good coat/carrying away stuff (Bellamy?) might have hidden it.
Apparently Seinfeld used that with a pregnant actress for half a season:
Julia Louis-Dreyfus's off-screen pregnancy meant that her character had to spend the latter half of this season hiding her belly behind furniture and laundry baskets.
from an Internet Archive snapshot of Sony Picture's website