The climate of the San Benito appellation is generally moderate, cooled by Pacific Ocean breezes that penetrate through gaps in the Gabilan and Santa Lucia mountain ranges.

However, climatic generalizations don't do justice to this viticultural area, as wide variations in elevation and soil structure provide unique microclimates.  For example, the Mt. Harlan Vineyard is at an altitude of 2,300 feet and is in one of the coolest regions in California.

A method for classifying wine climate regions that was developed in the 1930s at the University of California at Davis by Professors A. J. Winkler and Maynard Amerine. This system is referred to variously as degree days, heat summation method, Winkler Scale, and Regions I-V.  The method is based on the theory that no vine shoot growth occurs below 50°F and that each degree a day averages above 50°F is considered a degree day.  For example, if during a 24-hour period the temperature ranges from 57° to 81°F, the average is 69°F, which is equivalent to 19 degree days (69 minus 50).  The heat summation (sum of all the degree days between April 1 and October 31) of a growing region determines its classification, which is described in total degree days.  There are five climate region classifications, which suggests that California has growing environments that are comparable to the various traditional winemaking regions throughout the world.

• Climate Region I (up to 2,500 degree days) is the coolest and is similar to regions like Champagne and Côte D'Or in France and the Rhine in Germany.  It includes portions of the following areas: Anderson Valley, Carneros, Edna Valley, Marin, Mendocino, Monterey, Napa, Russian River Valley, Santa Clara, Santa Cruz Mountains, and Sonoma. Suggested varieties for Region I include Cabernet Sauvignon, Chardonnay, Pinot Noir, Riesling, and Sauvignon Blanc.

• Climate Region II (from 2,500 to 3,000 degree days) is similar to France's Bordeaux region and includes portions of the following areas: Alexander Valley, Anderson Valley, Chalk Hill, Edna Valley, Mendocino, Monterey, Napa, Potter Valley, Russian River Valley, Santa Clara, and Sonoma. Suggested varieties include those for Region I plus Merlot.

• Climate Region III (from 3,000 to 3,500 degree days) is equivalent to France's Rhône region and includes portions of the following areas: Alameda, Alexander Valley, Contra Costa, El Dorado, Knights Valley, Lake, McDowell Valley, Mendocino, Monterey, Napa, Paso Robles, Placer, Redwood Valley, Riverside, San Benito, Santa Clara, and Sonoma. Suggested varieties include Carignan, Ruby Cabernet, Sauvignon Blanc, Semillon, and Zinfandel.

The authors of this approach have acknowledged that within these broader regions there are microclimates capable of growing ither varieties.