During 1999, tropical cyclones formed in seven major bodies of water, commonly known as tropical cyclone basins. Tropical cyclones will be assigned names by various weather agencies if they attain maximum sustained winds of . During the year, one hundred thirty-two systems have formed and a record-low a sixty-five were named. The strongest tropical cyclone of the year was Gwenda, attaining maximum sustained winds of and a pressure of , later tied with Inigo in 2003. The costliest tropical cyclone of the year was Floyd, with around $6.5 billion worth of damages as it affected the Bahamas, the East Coast of the United States, and Atlantic Canada, while the deadliest tropical cyclone of this year was a tropical cyclone in Odisha, which was blamed for over 9,667 deaths as it devastated India. Among this year's systems, twenty-one became major tropical cyclones, of which three intensified into Category 5 tropical cyclones on the Saffir–Simpson scale (SSHWS). The accumulated cyclone energy (ACE) index for the 1999 (seven basins combined), as calculated by Colorado State University (CSU) was 606.4 units, which was below the 1991–2020 mean of 770.2 units.

The most active basin in the year was the Western Pacific Ocean, which had 19 named systems, including one system that crossed from the Central Pacific. The North Atlantic Ocean had an above-average and destructive season, with 12 named storms forming; eight of those became hurricanes, and five Category 4 hurricanes – the highest number recorded in a single season in the Atlantic basin, previously tied in 1933 and 1961, and later tied in 2005 and 2020. The Eastern Pacific had a total of nine named storms; six of those became hurricanes. The North Indian Ocean was extremely active and deadly tropical cyclone season in recent times, with four named storms forming, producing the fifth-most accumulated cyclone energy in this basin on record. Activity across the Southern Hemisphere's three basins (South-West Indian, Australian, and South Pacific) was fairly significant, with the regions recording twenty-one named storms altogether, with the most intense Southern Hemisphere cyclones of the year, Cyclone Gwenda and Cyclone Vance in the Australian region, peaking with a central pressure of .

Tropical cyclones were primarily monitored by ten warning centers across the world, which are designated as a Regional Specialized Meteorological Center (RSMC) or a Tropical Cyclone Warning Center (TCWC) by the World Meteorological Organization (WMO). These ten centers are the National Hurricane Center (NHC) and the Central Pacific Hurricane Center (CPHC), Japan Meteorological Agency (JMA), Indian Meteorological Department (IMD), Météo-France (MFR), Indonesia's Meteorology, Climatology, and Geophysical Agency (BMKG), the Australian Bureau of Meteorology (BoM), Papua New Guinea's National Weather Service (PNGNWS), the Fiji Meteorological Service (FMS), and New Zealand's MetService. Unofficial, but still notable, warning centres include the Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA), the United States's Joint Typhoon Warning Center (JTWC), and the Brazilian Navy Hydrographic Center.

Global atmospheric and hydrological conditions A strong La Niña was present for the whole year, which made the Atlantic and North Pacific waters warmer than usual.

Summary

North Atlantic Ocean

The Atlantic hurricane season officially began on June 1, 1999, and the first tropical cyclone developed on June 11. It was an above–average season in which 16 tropical cyclones formed. Twelve depressions attained tropical storm status, and eight of these became hurricanes. Five hurricanes intensified further into major hurricanes. The season featured a record-tying five Category 4 hurricanes, later tied again in 2005 and 2020. These were Bret, Cindy, Floyd, Gert, and Hurricane Lenny. The last storm of the season, Hurricane Lenny, dissipated on November 23, which was about a week before the official season ending on November 30, 1999. A persistent La Niña that developed during the previous season was attributed to the above average activity. Between August and October, there was very low wind shear over the Caribbean Sea and western Atlantic Ocean, attributed to a combination of abnormal upper-level easterly winds and low-level westerly winds. Six hurricanes and two tropical storms made landfall during the season and caused at least 123 deaths and approximately $8.19 billion in damage. Hurricane Gert also caused damage and fatalities, despite not making landfall.

Overall, the season's activity was reflected with a high cumulative accumulated cyclone energy (ACE) rating of 177.

The most significant storm of the season was Hurricane Floyd, a strong Category 4 hurricane that caused devastating flooding along the East Coast of the United States, especially in North Carolina. Damage from the storm totaled approximately $6.5 billion (1999 USD) and there were at least 77 fatalities, making it the deadliest hurricane in the United States since Hurricane Agnes in 1972. Flooding from Floyd in North Carolina followed Hurricane Dennis, a slow and erratic–moving storm that dropped heavy rainfall in the eastern portion of the state. Tropical Depression Eleven in October contributed to extreme flooding in Mexico, which left 636 people dead and caused $491.3 million in damage, though impact could not be distinguished from the storm itself. Hurricane Irene caused extensive flooding in Cuba and Florida, with lesser effects in the Bahamas and North Carolina. Irene was the second–costliest storm of the season, with about $800 million in damage. Hurricane Lenny was an unusual eastward–moving storm in the Caribbean Sea and a strong late–season storm. It caused extensive damage in the Lesser Antilles in the month of November.

Eastern and Central Pacific Ocean

The 1999 Pacific hurricane season officially started on May 15, 1999 in the eastern Pacific, and on June 1, 1999, in the central Pacific, and lasted until November 30, 1999. These dates conventionally delimit the period of each year when most tropical cyclones form in the northeastern Pacific Ocean. The 1999 Pacific hurricane season was well below average, due to the strong La Niña that was occurring at the time, which causes wind shear to be increased and water temperatures to decrease, resulting in conditions less conductive for tropical cyclones in the East Pacific. There were 14 cyclones in total, including 5 unnamed tropical depressions. Of these, 9 became a tropical storm, while 6 reached hurricane status. Further, 2 of these became major hurricanes, which is Category 3 intensity or higher on the Saffir-Simpson hurricane scale.

Tropical cyclogenesis began with Hurricane Adrian, which developed on June 18. Although it remained offshore, Adrian brought rough surf and flooding to Mexico, which resulted in 6 fatalities. The storm peaked as a Category 2 before dissipating on June 22. No other tropical cyclones formed in June. Activity halted until July 9, when Hurricane Beatriz developed. Though it peaked as a Category 3 hurricane before dissipating on July 17, the storm caused no damage on land because it remained well offshore. The next system, a short-lived Tropical Depression Three-E, did not result in impact as a tropical cyclone, though the precursor brought heavy rainfall and gusty winds to Central America. Tropical Depression Four-E, was the first of three cyclones to cross into the Central Pacific Hurricane Center's area of responsibility, which is between 140°W and the International Date Line. Two other short-lived system in July, Tropical Storm Calvin and Tropical Depression Six-E, caused no damage. In August, Hurricane Dora, the strongest storm of the 1999 Pacific hurricane season, produced gusty winds and large waves on Johnston Atoll and the island of Hawaii, though minimal damage was left in its wake. After crossing the International Date Line on August 20, Dora became the first tropical cyclones to exist in all three basins of the North Pacific – Eastern, Central, and Western – since Hurricane John in 1994. Hurricane Eugene also existed in the Eastern and Central Pacific, but dissipated on August 15 while south of the main Hawaiian Islands, well before reaching the International Date Line. Nonetheless, it produced up to of rainfall on the Big Island of Hawaii. In the remainder of August, there was a series of short-lived tropical cyclones that did not effect land, including Tropical Depression Nine-E, Tropical Storm Fernanda, and Tropical Depression Eleven-E.

During the month of September, the deadliest tropical cyclone of the season, Hurricane Greg, was spawned near the Pacific coast of Mexico. Greg which killed 10 people when it made landfall on southern Baja California. The hurricane and its precursor produced heavy rainfall across much of Mexico, with the highest total reaching . The heavy rains damaged or destroyed more than 2,000 homes. The remnant moisture from the system, combined with an area of low pressure, resulted in strong thunderstorms across California, which led to numerous power outages, damage to homes and vehicles, and started many wildfires. The other in the month of September was Hurricane Hilary, a storm that approached Baja California, but dissipated offshore on September 21, resulting in no impact. The final system, Tropical Storm Irwin, produced scattered areas of heavy rainfall over Mexico in October, but caused no significant flooding. It dissipated on October 11, over a month and a half before the official end of the season on November 30. In addition to the systems observed by the CPHC and NHC, a tropical depression formed east of the International Dateline on August 19, and quickly exited CPHC's area of responsibility; however, this storm was not included into CPHC database.

Western Pacific Ocean

It was the last Pacific typhoon season to use English names as storm names. It also featured the lowest number of typhoons on record, with only five reaching this intensity. This was mainly due to a strong La Niña which persisted from last year. It also featured the least amount of ACE produced on record. The season was also below-average in named storms, with only 20 of such spawning. This season also featured multiple landfalls in Hong Kong, but it was much more active than the previous season. The first named storm, Hilda, developed on January 6, while the last named storm, Gloria, dissipated on November 16.

North Indian Ocean

It was an extremely active and deadly tropical cyclone season in recent times. The season produced an above-average number of cyclonic storms but there was a very above-average number of intense cyclones. In May, a Category 3 cyclone struck Pakistan, leaving 6,400 people dead. In October, two very intense cyclones struck eastern India within two weeks of each other with the latter becoming the most intense Northern Indian Ocean cyclone on record, leaving over 10,000 people dead and causing more than $5.4 billion (1999 USD) in damages.

South-West Indian Ocean

January–June