"The main roads between Laayoune and Tan-Tan (700 kilometres, 434 miles southwest of Rabat) and Laayoune and Smara were reopened Sunday at dawn in both directions to trucks travelling in convoys of 20," the source said.
Passenger traffic has also resumed.
Torrential downpours lashed the area Tuesday and Wednesday and caused floods along two normally dry watercourses on a scale not seen for decades, according to local people quoted by the Moroccan MAP press agency.
Water up to one metre (three feet) deep had inundated houses and cut roads in and around Laayoune, local people said.
Western Sahara was annexed by Morocco in 1975 after Spain gave up its rule of the phosphate-rich region. Sovereignty is claimed by the Polisario Front, which fought a lengthy guerrilla war against Rabat's forces before a ceasefire in 1991.