Authorities of the US charity Mercy Corps say humanitarian agencies are concerned about those vulnerable to disease in Dolow.
In an interview with AFP, Mohamed Dahir, the water and sanitation officer at Mercy Corps, said "the possibility for malaria outbreak is high due to the mosquitos, and there are also concerns about watery diarrhea breaking out due to the possible contamination of the water system."
"We still don't know exactly the level of contamination but what we have seen is the leaked septic tanks and destroyed toilets of the affected neighborhood which contaminate the water wells," Dahir added.
The UN humanitarian agency OCHA said in an update last week that 33 districts of Somalia had been deluged, with a significant increase in cases of Acute Watery Diarrhea, AWD, or cholera and a rise in malaria cases.
It said there were concerns that contaminated stagnant water around schools poses a "serious risk" of waterborne diseases for school children.
Shukri Abdi Osman, a 34-year-old mother of three, who shelters in a camp for the displaced in Dolow with her children, said, "I have never seen such devastating floods before, everything happened quickly."
"When we realized the water was coming it was too late to collect all our belongings. We left our houses at midnight and all we were able to grab was our children," she added.
The 34-year-old mother said,"the toilets were destroyed and even the tap water is now mixed with the dirty flood water which includes leaking septic tanks."
Osman further expressed fears that her daughter might have contracted malaria and typhoid.
Sadia Sharif Hassan, a 40-year-old mother of seven, based in a Dolow IDP camp said, "the most important thing is to save the lives of our children," adding that her family barely had enough food to eat each day.
"The mosquitos are relentless and several of my children are already feeling unwell, they are suffering from fever... all their bodies are covered with bites now," Hassan said.
In Garboolow, 70-year-old Owliyo Mohamed Abdirahman almost slipped and fell in the mud as she tried to rescue belongings from her damaged corrugated metal home but found everything had been swept away.
“This is what is left of my house in which I lived with my son who is sick now, his children and his wife," she said in despair. "We ran away with our lives and carried nothing else."
She and her family are having to rely on the kindness of well-wishers who have provided food and clothing.
Garboolow commissioner Mursal Mohamed Adan said the authorities are waiting anxiously for help from aid agencies.
"God knows better what is next, but we are still concerned if rains continue to cause more flooding it will only make the situation worse."
Somali authorities have declared a state of emergency over what the United Nations has called "once-in-a-century" flooding, with almost 100 lives lost across the country and 700,000 people made homeless.
Torrential rains linked to the El Nino weather phenomenon have lashed the Horn of Africa on the heels of the worst drought in 40 years that drove millions to the brink of famine in Somalia.
Somalia is considered one of the most vulnerable countries to climate change, locked in a vicious cycle of drought and floods. The Horn of Africa nation is particularly ill-equipped to cope with the crisis as it battles deep poverty and a deadly Islamist insurgency.
In one of the worst El Nino episodes, in late 1997 and early 1998, at least 1,800 people died in Somalia alone when the Juba River burst its banks.
The latest floods have washed away homes, schools, farmland, roads and bridges, leaving many without shelter, food or clean drinking water.