I noticed on my boat i recently bought that the paint is bubbling and chipping away along the water line on the port and starboard side. There are little bubbles about 1mm in diameter. and you can see gray primer underneath once it chips off. The bottom of the boat does not have this problem, or anywhere else only on the sides where the water is contacting when the boat is wet. The boat is used in fresh water and and has been its whole life I would assume.

How long have you owned the baot ? most likely the boat was repainted from the water line up - aliphatic acrylic polyurethanes do not like continous water contact and bubbles or blisters will occur.

one month, the longest it has been in the water is 4 hours at one time. It seems strange the bottom wasnt painted, just the waterline on the sides. what can i do to fix it, does the whole boat need to be painted?

not uncommon to paint from the hard chine up. as a rule (atleast with me) its no paint below the hard chine or waterline if possible. unfortunatly on complete re sprays there is usually a long triangle of paint that will see immersion though. Usually it isnt a problem on boats that see limited stays in the water. What is the overall condition of the finish? I have seen budget products have problems but never with something along the order of PPG's 2021 or like clears. it may be a problem that was covered up before you purchased it. In other words it may have see long term stays in the water and blistered than those were covered up to help sell the boat. all is not lost though it is certainly correctable.

Overall it looks good, but the problem is in the long triangle. It is noticeably worse each time i use the boat. I cannot say if it had the blisters or not before I took the boat home, but it didnt have any of the paint chipping off for sure at that time. I've used the boat 10-15 times this season. I bought the boat off ebay from a used car dealer, so who knows.