The climate of Pinnacles is typical of the Mediterranean climate of California, with cool wet winters and hot dry summers. Summer temperatures of over 100 degrees are common, but coastal fog will often come into the valleys at night. Nighttime summer temperatures of 50 degrees are common, making for enormous daily temperature swings.

Winter climate is akin to the California deserts, with mild days and nights often dropping into the low 20s. The average precipitation is approximately 16 inches per year. Nearly all of the precipitation is in the form of rainfall, with the majority occurring from December to March. Snowfall is rare, but does occur in significant amounts about every 10 years.

The great variability in seasonal precipitation is due to the east Pacific high. This dominant weather feature shifts northward in the summer to shunt storms far to the north. Occasionally this feature brings subtropical moisture into central California from southerly latitudes, producing one to five thundershowers per year in the Monument. Mostly, however, the east Pacific high acts as a giant valve completely shutting off precipitation for long stretches of the year.

California is known for its long dry and wet cycles. Changes in the East Pacific high shift on approximately a six-year cycle. The result is persistent drought for five to eight years, followed by a wet period. Such cyclic variation is an important consideration in vegetation, wildlife, and water management.