Unlike other parts of Indonesia, weather in Raja Ampat is relatively stable all year around, consistently around 25-32°C, with high humidity at times causing it to feel hotter.

Although there is a typical dry season, rainy season and windy season, the below is a general guideline to seasonal patterns in Raja Ampat.  Many of the islands (especially the 4 big islands of Salawati, Batanta, Waigeo and Misool) have microclimates that vary substantially from islands nearby. There is a surprising amount of variation in local weather conditions; these microclimates can lead to sunny days in Gam, whilst watching rain pouring over nearby islands of Kri or Waigeo.

October – April:
The ideal time to visit based on dryer weather and calmer wind.  It is also during this period that manta rays are present in the northern region of Raja Ampat.

July and August (sometimes June-Oct):
In this period the usually calm seas can get rough due to a southerly wind. Liveaboards suspend their operations in Raja Ampat at this time, and some dive resorts and homestays may cancel dives or find diving conditions rough due to wind, choppy waters or even waves in some locations.

July/August and Nov/December:
This is considered rainy season, where the likelihood of tropical rains is higher.  However, these rainy seasons are not characterised by heavy monsoonal rains like other locations in Indonesia, but rather an increased likelihood of tropical rain or storms that pass within a few hours.