Television footages showed dramatic scenery in Beira were roads have been transformed into rivers and many homes including vehicles covered by waters and trees uprooted.
This follows a tropical storm that is sweeping across the central provinces of Sofala and Zambézia.
Dondo is in the same situation with flooded homes, impassable streets and people in despair.
The residents complain that they have not received any kind of support from the authorities.
"We are stranded here and there is no sign of relief authorities taking take ofus", One resident told the provate television station Stv.
Like many African coastal cities, Beira, which lies just above sea-level, is in a race against time to protect itself from cyclones, floods and rising sea-water levels.
Experts say climate change will increase the severity of cyclones and flooding, particularly along the country’s 2,700 kilometers of coast.
The National Meteorological Institute has issued a statement warning of a moderate tropical storm named "Desmond", accompanied by heavy rains, which had already hit several districts and municipalities in Sofala.
During heavy downpours in the rainy season, from November to March, Beira’s ageing drainage system backs up within hours, forcing many people out of their homes, in particular in the slums.
As a result, year after year, residents loose their livelihoods and are exposed to diseases like malaria and cholera and drinking water can become contaminated due to fecal material being swept out.
With a master plan now drawn up to make Beira more resilient and sustainable by 2035, Municipal authorities are oping a partnership between the city and private investors will help him to raise the $100 million estimated it will cost to disaster-proof the city.