The global climate during 1999 was impacted by Pacific cold episode (La Niña) conditions throughout the year, which resulted in regional precipitation and atmospheric circulation patterns across the Pacific Ocean and the Americas that are generally consistent with those observed during past cold episodes. The primary La Niña-related precipitation anomalies included 1) increased rainfall across Indonesia, and a nearly complete disappearance of rainfall across the east-central and eastern equatorial Pacific; 2) above-normal rains across northwestern and northern Australia; 3) increased monsoon rains across the Sahel region of western Africa; 4) above-average rains over southeastern Africa, 5) above-average rains over the Caribbean Sea and portions of Central America, and 6) below-average rains in southeastern South America.

The La Niña also contributed to persistent cyclonic circulation anomalies in the subtropics of both hemispheres, which flanked the area of suppressed convective activity over the eastern half of the equatorial Pacific. In the Northern Hemisphere this anomaly feature contributed to a pronounced westward retraction of the wintertime East Asian jet stream, which subsequently impacted precipitation and storm patterns across the eastern North Pacific and western North America. The La Niña-related pattern of tropical rainfall also contributed to a very persistent pattern of anticyclonic circulation anomalies in the middle latitude of both hemispheres, extending from the eastern Pacific across the Atlantic and Africa eastward to Australasia. This anomaly pattern was associated with an active Atlantic hurricane season, an inactive eastern North Pacific hurricane season, above-average rains in the African Sahel, and an overall amplification of the entire southeast Asian summer monsoon complex.

The active 1999 North Atlantic hurricane season featured 12 named storms, 8 of which became hurricanes, and 5 of which became intense hurricanes. The peak of activity during mid-August–October was accompanied by low vertical wind shear across the central and western Atlantic, along with both a favorable structure and location of the African easterly jet. In contrast, only 9 tropical storms formed over the eastern North Pacific during the year, making it one of the most inactive years for that region in the historical record. This relative inactivity was linked to a persistent pattern of high vertical wind shear that covered much of the main development region of the eastern North Pacific.

Other regional aspects of the short-term climate included: 1) above-average wintertime precipitation and increased storminess in the Pacific Northwest, United States; 2) above-average monsoonal rainfall across the southwestern United States; 3) drought over the northeastern quadrant of the United States during April–mid-August; 4) hurricane-related flooding in the Carolinas during September; 5) drought over the south-central United States during July–November; 6) below-average rainfall in the Hawaiian Islands throughout the year, with long-term dryness affecting some parts of the islands since October 1997; 7) a continuation of long-term drought conditions in southeastern Australia, with most of Victoria experiencing below-average rainfall since late 1996; and 8) above-average rainfall in central China during April–August.

Global annual mean surface temperatures during 1999 for land and marine areas were 0.41°C above the 1880–1998 long-term mean, making it the fifth warmest year in the record. However, significant cooling was evident in the Tropics during 1999 in association with a continuation of La Niña conditions. In contrast, temperatures in both the Northern Hemisphere and Southern Hemisphere extratropics were the second warmest in the historical record during 1999, and only slightly below the record 1998 anomalies.

The areal extent of the Antarctic ozone hole remained near record levels during 1999. The ozone hole also lasted longer than has been observed in past years.