Severe Tropical Cyclone Rona was the only cyclone to threaten and impact on the Queensland coast during the 1998-99 season. A tropical low embedded in an active monsoon trough was evident off the north Queensland coast on 9 February. Strong westerly winds persisted around the northern side of the low, however a deep low pressure system off the southern Queensland coast brought a weak pressure gradient and only light winds to the southern side of the system.
A middle to upper level trough over eastern Australia steered the low slowly eastwards, but by late on 9 February this began to weaken and within 24 hours had dissipated. This allowed strong ridging to develop south of the system, with the easterly trade winds extending northward to the monsoon trough. Coincident with ridging to the south of the system, pressures rose over New Guinea, strengthening the pressure gradient between New Guinea and the tropical low.
The upper pattern in the region of the low became highly favourable for development with a strong easterly outflow channel forming on the equatorward side of the system, and strong northwest flow on the poleward side ahead of an amplifying upper trough over central Australia. In response, the low rapidly intensified to be named tropical cyclone Rona at 1800 UTC on 10 February, located about 310 km east of the north Queensland coast. At this time the system had commenced moving southwest and then turned on a more westerly track as the middle level ridge strengthened.
Rona continued to intensify over the next 6 to 12 hours and was upgraded to storm force with estimated MSW of 93 km/h at 0400 UTC and hurricane force with estimated MSW of 119 km/h at 0700 UTC on 11 February. By this time the middle level ridge to the south of the system strengthened further and in response Rona moved rapidly west-northwest towards the Queensland coast. Radar imagery (from the Cairns radar to the south of the cyclone eye) displayed a ragged, diffuse eye, however, the signal may have been attenuated somewhat by deep convection on the system's southern side. Between 1219 UTC and 1246 UTC on 11 February, Low Isles reported MSW in excess of 108 km/h, peaking at 134 km/h at 1228 UTC with a maximum gust to 159 km/h. The system eye was located about 23 km north of Low Isles at this time, however radar imagery is inconclusive in determining if the observation site experienced the radius of maximum winds. The minimum station pressure recorded at Low Isles was 983 hPa at 1216 UTC.
Rona crossed the coast just to the north of Cow Bay near the mouth of the Daintree River around 1300 UTC on 11 February. The system continued to track west-northwest over land and maintain cyclone intensity until 1800 UTC on 11 February at which time it was downgraded to a tropical low. A definite low level centre was difficult to track beyond this time, with several small scale centres developing. However, the 850 hPa circulation could be traced for several days as it tracked eastward across the Coral Sea to eventually become tropical cyclone Frank .
Significant wind damage from Rona extended from Newell Beach to Cape Tribulation with the major damage occurring between Cape Kimberley and Cape Tribulation on the northern side of the coastal crossing location. Some trees in the Cape Tribulation area that survived an intense cyclone in 1934 were felled by Rona . As the system crossed the coast in a sparsely populated area of the north Queensland coast, structural damage to property was minimal. Heavy rainfall following the landfall of Rona resulted in flooding from Cairns to Townsville. Highest 24 hour rainfall totals to 2300 UTC on 12 February were 531 mm at Topaz, 474 mm at Greenhaven, and 420 mm at Kuranda. A 1 m storm surge was recorded at Port Douglas (occurring at low tide) while at the Mouth of the Mossman River (near Newell and south of the radius of maximum winds) a 1.4 m storm surge was measured. Peak significant wave heights recorded at Low Isles exceeded 3.5 m with a maximum wave height in excess of 6.3 m.