Seroja brought historic flooding and landslides to portions of southern Indonesia and East Timor and later went on to make landfall in Western Australia's Mid West region, becoming the first to do so since Cyclone Elaine in 1999.

The low intensified into Tropical Cyclone Seroja by 4 April, while it was passing north of Rote Island, while continuing its slow strengthening trend.

Due to the presence of Tropical Cyclone Odette in Seroja's vicinity, interaction was anticipated as the storm moved away from Indonesia and East Timor.

[9][10] The cyclone damaged or destroyed more than 20,000 houses and five bridges in Indonesia's East Nusa Tenggara province while more than 12,000 people were evacuated to government-owned shelters.

[26] The low drifted close to the coast of Timor very slowly with persistent spiraling bands of convection occupying the storm's circulation, producing prolific rainfall in the surrounding regions on 3–4 April.

[29] Although there were fluctuations in central convection, a favorable environment of deep moisture, low vertical wind shear, and good outflow meant further development of the system was expected.

The storm intensified to a Category 2 tropical cyclone at 19:00 UTC, with 10-minute sustained winds of 105 km/h (65 mph) and its central pressure deepening to 982 mb (29.00 inHg).

[33] Seroja held this strength for roughly 12 hours, before unexpectedly weakening to a Category 1 tropical cyclone yet again on 6 April, due to southeasterly wind shear, and dry air partially exposing the low level circulation (LLC) and degrading its thunderstorm activity.

[36] Seroja resumed intensification by the next day, re-intensifying into a Category 2 tropical cyclone at 13:16 UTC on 9 April, as the storm began to absorb Odette and as wind shear started to ease off.

[37] By 10 April, Seroja had absorbed most of Odette's remaining thunderstorms and began to accelerate to the southeast towards Western Australia, maintaining a relatively organized structure.

[52][53] A tropical cyclone warning was then issued for Cape Cuvier to Geraldton on 10 April as Seroja neared, albeit strengthening slower than anticipated.

All people between Coral Bay and Geraldton were eventually told to evacuate immediately on 11 April as homes were not built to withstand such high winds.

[17] According to a report published in January 2022 by the United Nations Office for Disaster Risk Reduction (UNDRR), the flooding in East Timor affected 13 municipalities and 30,322 households, destroyed 4,212 houses, took 34 lives, and was "... said to be the worst the country has seen in 50 years ...".

[67] The country manager of Australian People for Health, Education and Development Abroad (APHEDA) attributed it to the obstruction of waterways by housing erected along them.

[73][74][58] In the East Flores Regency, fourteen villages were hit by flash flooding as a result of runoff of volcanic materials from Mount Ile Lewotolok.

[98] Farmers in the seaweed industry in Kupang Regency lost an estimated 7 billion rupiah (US$484,000) due to crop failure and destruction of cultivation facilities/infrastructure attributed to Seroja.

[99] Total preliminary estimated losses in East Nusa Tenggara, according to the Indonesian National Board for Disaster Management, amounted to at least 3.4 trillion rupiah (US$236 million) as of May 2021.

[16] After Seroja made landfall, around 4,350 people in Western Australia lost electricity as the storm's high winds downed power lines, particularly around Kalbarri.

[112] Access and communication to towns further north impacted by the cyclone, such as Geraldton, were cut off, leaving the scale of damage in the city largely unknown.

[114][113] During the cyclone, one person died; a 38-year-old maintenance worker who was electrocuted in Coral Bay after attempting to secure a caravan park's private power pole which had fallen down in the wind.

[119] East Timor Prime Minister Taur Matan Ruak cited the floods as one of the most devastating incidents to affect the country in 40 years.

[6] In addition, the government asked the World Bank for support in assessing damages, and advice on longer-term implications for disaster risk management.

[121] The leader of Fretilin, Mari Alkatiri, urged East Timor government to ask for more international assistance such as helicopter and military cargo.

[6] The Government of East Timor reintroduced COVID-19 lockdown on three cities; Dili, Baucau, and Viqueque amid rising infection case after the disaster until 2 May.

[133] The chief of the Indonesian National Board for Disaster Management (BNPB), Doni Monardo planned to visit the affected regions on 5 April 2021.

[147] The People's Representative Council urged the government to speed up the distribution of relief and suggested using Indonesian army personnel to help overcome logistical hurdles.

[158] COVID-19 Task Force personnel were sent to the affected regions and shelters to limit the spread of COVID-19, using experience from 2021 South Kalimantan floods and 2021 West Sulawesi earthquake.

[176] Despite calls from several prominent public figures in the province to declare Cyclone Seroja as a national disaster,[177][96] Governor of East Nusa Tenggara Viktor Laiskodat refused to do so, stating that efforts from the central government were sufficient to meet the needs of the survivors.

[179][180] WALHI pressured the provincial government of the province of East Nusa Tenggara to declare a state of emergency and criticized the lack of a response from the governor there, Viktor Laiskodat.

[186] A member of the Indonesia National Student Movement from the region harshly criticized the local government and asked the President to directly see and discipline them.