In the earlier episodes Clarke is shown to have sex with Finn and Bellamy. But in the later series Clarke is shown as lesbian. In season 4 last episode Clarke is shown having a girl.
So when did Clarke become pregnant?
There's no specific indication that Maddie is Clarke's daugher (barring advanced aging) since she is clearly more than 6 years old (less pregnancy time).
Jason Rothenburg, producer of The 100...
We wanted a reveal that Clarke survived and that her Nightblood kicked in, and she's now essentially — or so we think for the first couple of minutes of that final pop-out at the end — the lone survivor on the planet. Her friends... we know they made it to space, but she doesn't know whether or not they made it. We also know there's a group of 1200 led by Octavia (Marie Avgeropoulos) in the bunker, but Clarke is the lone survivor on the planet. And then we reveal she's found Maddy, this Nightblood child. Clearly, there's a maternal connection between the two of them when we reveal her in the end.
They have been together for years when we first see them. She's been with Maddy alone for a number of years; longer than she was ever on the ground with anybody. So it's going to be a very powerful bond and a huge part of season five.
Found does not indicate a daughter at least not a birth-daughter.
Indeed...at another interview...Rothenberg confirms
The mother-daughter vibe that you pick up on in that scene is real. (It’s not her biological child; I think it’s fairly obvious that the kid is too old for that.) But she is a nightblood. Clarke was alone until she found Madi. When we find them together in [episode] 413, they have been together already for a number of years and are relying on each other and surviving together.
As for who Maddy/Madi (the spelling varies) is and where she comes from is yet to be revealed in S5.