Well, without specific details of the case (make/model?), 120mm does not fit in 90mm.
So no, it won't fit.
okay, il be more specific,
i have a Medion Akoya E4090 D (MD 8310). on the backside there is a rear fan slot free for a 90mm fan.
So can i build in a water cooler for my cpu and attach a 120mm fan to the rear fan slot?
No, the 120mm water cooler will not fit in the space for a 90mm fan. A better option is to use a tower cooler or some other sort of air cooler, installing a 90mm fan in the back.