Weather will likely play an important role when you plan your trip to San Juan, and keep in mind that cheaper options are usually available when the weather isn't as good. The hottest months are usually May and June with an average temp of 79°F, while the coldest months are January and February with an average of 73°F. The rainiest months in San Juan are November, October, September, and August, with each month seeing an average of 11 inches of rainfall.