Kwajalein’s location gives it a tropical marine climate. The atoll experiences a relatively dry windy season from mid-December to mid-May and a relatively wet calm (wind) season from mid-May to mid-November. Normal annual rainfall is approximately 100 inches; approximately 72% of the annual rainfall occurs during the wet season and 28% occurs during the dry season. On average, the prevailing wind direction is from the east-northeast during the entire year, although, winds may become more variable during the wet season, when occasional southerly or even westerly winds occur. Average wind speed is near 17 mph from December to April and near 12 mph from May to November.

The average daily maximum temperature is 86.5ºF; the average minimum is 77.6ºF. The extreme temperatures are 97ºF and 68ºF. Average relative humidity ranges from 83% at local noon to 78% at midnight.

Although most of the rainfall at Kwajalein comes from showers, thunderstorms are infrequent. On average, thunderstorms occur fewer than 12 days each year. The frequency of thunderstorms ranges from 0.1 per month from January to March to 2.0 per month in September. During the modern era of record keeping, since 1919, a fully developed typhoon has never struck Kwajalein Atoll; however, tropical storms (sustained winds of 40 to 74 mph) impact the atoll about once every four to seven years on average.