Ishigaki is subtropical, which means it is warm year-round and genuinely hot from June through September. The best time for diving and snorkelling is March to May: water temperatures are comfortable at around 24°C, visibility is high, and the summer crowds haven't yet arrived. The rainy season (tsuyu) runs from May into June.
Typhoon season runs from July through October, and typhoons do directly hit the island — not frequently, but seriously when they do. Travel insurance and flexibility in your plans are wise. Winter (December to February) is warm by European standards, around 18–22°C, with occasional cool northerly winds. The sea can be rough in winter but diving is still possible on calmer days.
The Yaeyama Star Festival (Tanabata), celebrated here about a month later than on mainland Japan per the lunar calendar, falls in late August and is worth timing a visit around if possible.