Weather will likely play an important role when you plan your trip to San Blas Islands, and keep in mind that cheaper options are usually available when the weather isn't as good. The hottest months are usually June and September with an average temp of 80°F, while the coldest months are February and March with an average of 78°F. The rainiest months in San Blas Islands are October, August, July, and November, with each month seeing an average of 12 inches of rainfall.