My middle child had this problem. For her it turned out to be an Upper Respiratory Infection and antibiotics cleared it up, but it did recurr quite a few times and she continued to be prone to these URI’s/sinus infections until she to to be about 3 or 3 1/2. It’s actually very common for newborns to be congested (I forgot the reason why), but for it to persist for three months would concern me.
Also, my firstborn had chronic nasal congestion which started when I started supplementing with formula, and I eventually found the congestion to be related to a milk allergy. Once I removed dairy from my diet and started supplementing with soy instead of milk formula, the nasal congestion stopped.