Abdirisaaq Mohamed Geriyow, executive director of the Social and Agricultural Development Organisation (SADO), an NGO based in Bardera, said the floods followed heavy rains in the town and in the hilly areas around it.
"We had 11 hours of very heavy rains on Monday [3 November]," he said.
Ahmed Aden Ahmed, district commissioner, said: "The floods displaced around 2,000 families [12,000 people] in and around Bardera and destroyed 500 hectares of farmland."
He said many of the displaced were staying with relatives in the town while many others had put up makeshift shelters in elevated areas around it.
Ahmed, whose family was also affected, said floods in the area were often caused by River Juba bursting its banks but this time it was the rains. "The last time we experienced anything like this was during 1998 el-Niño rains," he said.
The floods devastated Bardera's business centre, with many stores and offices now under water, Ahmed added.
He appealed for urgent help: "We need urgent help in shelter material, water and food."
He added: "It is not just the displaced but many businesses have been destroyed. The whole population is in a very tenuous position; we are concerned that the situation could deteriorate very rapidly."
Ahmed said the floods had also destroyed hundreds of latrines, creating a fertile ground for water-borne diseases.
Geriyow, who is an agronomist, told IRIN that most of those displaced "not only lost their homes but also their livelihoods. Many were farmers, and their farms and crops are under water."
He said the river was rising, creating fears of more flooding.
The rains are expected to continue through the end of October. Many parts of Somalia are experiencing the short "Deyr" rains (October-November).
Geriyow said downpours in neighbouring Ethiopia usually caused the rivers downstream in Somalia to swell, leading to the flooding.
The situation was exacerbated by the fact that since the collapse of the Somali government in 1991, no one has de-silted the riverbeds or managed the sluice gates on the rivers or adjoining canals, he said.
Local farmers had also cut into river embankments to irrigate their land, which contributes to flooding.