I am sorry your boy is not feeling well.He may have a urinary tract infection.
You are absolutely correct to be concerned, Not only can recurring infections damage your baby's urinary tract but his immune system as well.
UTI's must be treated with an effective broad spectrum antibiotic like Clavamox or clidamycin and for a long enough duration so all bacteria is eradicated. If not, they will refluorish, stronger and more resistant and reinfect him. In addition, the bacteria can become tolerant of the same antibiotic so the medication should be varied for best results.
He should also be encouraged to drink as much as possible to keep the kidneys and bladder flushed. You can give him one daily tsp of unsweetened (only) cranberry juice. That will reduce the PH of his urine and make his bladder inhospitable to UTI bacteria.
It is also possible these events may be triggered by stones or crystals. He should have a urine analysis so you will know for sure. Sometimes bacteria does not show up. If so he should still complete a round of antibiotics.
I would also check for sugar just to rule out diabetes.
Please let me know if you still have questions and how your baby is feeling. I will be happy to help further.
I hope he feels better very soon.