The region is now crowded with make-shift shelters that host thousands of refugees, who now rely on the goodwill of local residents.
Local leaders say they are overwhelmed by the number of displaced.
"This is a region devastated by two other displacements apart from the events in Mogadishu. We are also facing floods and drought in some parts. We are finding it increasingly hard to cope with the demands of the displaced."
A two-month-old Zakariya was born on the road between Jowhar and the capital.
Hawa Mohammed Ibrahim helped deliver him. She covered the 90km stretch on foot with 10 members of her family.
She told Al Jazeera: "We ran away for dear life, We just grabbed whatever we could and hit the road.
"We don't know what happened to the property we left behind in Mogadishu. We encountered so many problems on the way, one of the women I was with even had her baby by the roadside. We just ran."
The conflict in Somalia has created another problem, hunger.
The farmers in the Middle Shabelle Region of Somalia are now depending on food aid.
For the first time in 13 years they have had a poor harvest.
Aid agencies predict the worst for the people of southern Somalia as rains in neighbouring Ethiopia have swelled the River Shabelle flooding villages on the banks.
The rainy season expected shortly will not offer any respite.
The only hope for Somalis now, they say, is for calm to return to their country and for them to return to their normal life.