The dry season runs from May to October — this is the best time for diving and snorkelling, with calm seas, good visibility, and little rain. July and August are the busiest months, when domestic tourists from Java fill the guesthouses on weekends; if you visit then, try to come mid-week.
The wet season from November to April brings heavier rain and rougher seas. Crossings from Jepara or Semarang can be delayed or cancelled, sometimes for several days at a time. Water visibility drops and some dive sites become inaccessible. March and April see the transition back to calmer conditions and the islands are nearly empty.
If flexibility is not an option, May or June offer the best compromise: the dry season has arrived, the seas are calm, and the holiday crowds have not yet peaked.