Storms were officially tracked by the Météo-France office (MFR) on Réunion while the Joint Typhoon Warning Center (JTWC) in an unofficial basis.

Alibera meandered and changed directions several times before striking southeastern Madagascar on January 1, 1989, where it was considered the worst storm since 1925.

Gregoara attained peak winds of 170 km/h (110 mph) over the open waters of the Indian Ocean in March, although the JTWC considered Alibera to be stronger.

In April, Moderate Tropical Storm Hanta approached the northwest coast of Madagascar, but dissipated over the Mozambique Channel.

Using satellite imagery from National Oceanic and Atmospheric Administration, the agency estimated intensity through the Dvorak technique, and warned on tropical cyclones in the region from the coast of Africa to 90° E, south of the equator.

[2][7] Later, the precursor to Australian Tropical Cyclone Bessi was tracked in the eastern portion of the south-west Indian Ocean basin in the middle of April.

After drifting erratically for several days, the storm began a steady southwest motion on December 29 as a greatly weakened system.

[11] Upon moving ashore in Madagascar, the cyclone lashed coastal cities with heavy rainfall and up to 250 km/h (160 mph) wind gusts.

[15] By January 8, the system weakened to tropical depression status while looping back to the northwest,[14] steered by a ridge to the southwest.

[2] Cezera quickly intensified, and the JTWC upgraded it to the equivalence of a minimal hurricane on February 3 with 1‑minute peak winds of 150 km/h (93 mph).

[17] By February 4, Cezera began a Fujiwhara interaction with Tropical Cyclone Dety, which was located to the east; this caused the former storm to turn back to the northwest while gradually weakening.

Cezera briefly re-intensified into a moderate tropical storm on February 7, but weakened again on the next day while passing just north of St. Brandon.

[17] A tropical depression developed within the monsoon trough on February 2 to the southwest of Diego Garcia,[18][19] about 1,125 km (699 mi) east of Cezera.

[2] With an anticyclone – a high pressure area over the system – providing favorable conditions,[18] the depression quickly intensified while moving generally south-southwestward.

It executed a large loop and later turned back to the west due to a ridge to the south, during which it was named Walter by the BOM.

[24][25] However, the MFR did not begin issuing advisories until March 15, when Gregoara reached 85° E.[26] The JTWC classified the system as Tropical Cyclone 23S, which was a separate number from when the storm existed in the Australian basin.

[2] Gregoara moved to the southwest, intensifying into a tropical cyclone on March 16, the same day that the JTWC upgraded it to the equivalent of a minimal hurricane.

Three days later, Gregoara turned to the southeast as a weakened tropical depression,[26] subjected to cooler waters and stronger wind shear,[25] and it became extratropical.

[27] For several days, the system moved slowly over the southern Indian Ocean, turning to the southwest and later to the southeast before dissipating on March 27.

[28] On the next day, the JTWC classified it as Tropical Cyclone 27S with peak 1‑minute winds of 85 km/h (55 mph), although the agency did not include the name Hanta in advisories.

Hanta approached the northwest coast of Madagascar on April 14, passing within 11 km (6.8 mi) of the Anjajavy Forest before turning back to the west,[28] due to a ridge to the south.

[29] The final storm of the 1989-90 South-West Indian Ocean cyclone season formed as a tropical disturbance on May 11 west-southwest of Diego Garcia.

[2] After becoming a tropical storm, Ikonjo began a steadier westward movement, gradually curving back to the west-northwest, and bringing it just north of Agaléga on May 16.