The rainy season, known locally as invierno, or winter, extends from May to October. Almost all the annual rainfall occurs during this time, and yearly totals, particularly on southern-facing mountain slopes, can be as high as 2,000 millimeters (78.7 in). Protected areas and the central plateau receive lesser, although still significant, amounts. Rainfall during this season generally comes from low pressure over the Pacific and usually falls in heavy afternoon thunderstorms. Although hurricanes occasionally form in the Pacific, they seldom affect El Salvador, with the notable exception of Hurricane Mitch and Hurricane Emily in 1998.

From November through April, the northeast trade winds control weather patterns. During these months, air flowing from the Caribbean has had most of the precipitation wrung out of it while passing over the mountains in Honduras. By the time this air reaches El Salvador, it is dry, hot, and hazy. This season is known locally as verano, or summer.

Temperatures vary little with season; elevation is the primary determinant. The Pacific lowlands are the hottest region, with annual averages ranging from 25 to 29 °C (77 to 84.2 °F). San Salvador is representative of the central plateau, with an annual average temperature of 23 °C (73 °F) and absolute high and low readings of 38 and 6 °C (100.4 and 42.8 °F), respectively. Mountain areas are the coolest, with annual averages from 12 to 23 °C (53.6 to 73.4 °F) and minimum temperatures sometimes approaching freezing.