Climate in San Rafael consist of two pronounced seasons, the wet and dry.  The wet season starts around the month of May and ends around the month of November.  Normally the average annual rainfall is 1,518.6 mm with the months of July and August registering the harvest rainfall.

Occasional typhoons pass through the area especially during the months of June to September.  Cloudiness is heaviest during the months of July and September and lightest during the months of February and April.  June is the month when lightning occurs most frequently.  Thunderstorms occur most frequently during June and July.