The flooding occurred around the town of Kurtunwarey, 140km south of Mogadishu.
"In Afgoye Yarey alone, the population of some 1,750 families [about 10,500 people], were affected. Not a single resident is there now," Sidow Hassan Arkey, an elder, told IRIN on 19 November.
"We were about to harvest [crops] when the river broke its banks," Arkey added.
He said residents not only lost their crops but also their homes. "We are all in temporary shelters around our village."
Salad Ali Kofi, an elder from Kurtunwarey, the main town in the area, said residents had had poor harvests in the past two years and were expecting this year to be good. "We hoped for a good harvest but now everything is lost and the population needs help."
Abdirashid Haji, country director of Concern Worldwide, told IRIN some 15 villages, with an estimated population of 4500 families, or 27,000 people, were affected by the flooding.
Worst affected were Afgoye Yarey, Uran-Urow, Murqmal, Bulo Warabo, Aflow and Dhayni, said Haji, who visited the villages. "All seven villages are inaccessible." The villagers had moved to higher ground, or to unaffected areas, he said.
He said 7,927 hectares of farmland, including 6,313 of standing crops, were destroyed.
The floods also destroyed 15 water wells and 45km of irrigation canals. The rains were still continuing and level of water in the Shabelle was still rising, he said.
Fadumo SiidAli, 30, from Afgoye Yarey, told IRIN the villagers in her area had lost everything. "We have nothing, except the stuff they [Concern Worldwide] gave us."
She said she and her three children were living in a temporary shelter, with plastic sheeting.
Haji said his agency provided non-food kits to some 1,500 families, including plastic sheeting, blankets, mosquito nets and cooking utensils.
Making matters worse is the lack of proper management of the irrigation system since the collapse of the national government in 1991, he said.
"There has been little de-silting of the riverbed or proper managing of gates on the rivers or adjoining canals," he added. Farmers had also eroded the river bank in an effort to irrigate their fields.
The UN World Food Programme (WFP) said it was assessing the situation with a view to helping the affected population.
"WFP is assessing the situation in terms of the number of villages and people affected by the floods to provide them with necessary assistance," said Abdi Ibrahim Jama, information officer for WFP in Somalia.