"We sent our proposals to North Korea today calling for talks on the peaceful use of the river and preventing possible damage from flooding," Lee Jong-Joo, a ministry spokeswoman, told AFP.
Ministry officials said that the South had also proposed that Red Cross societies of the two sides hold separate talks on Friday to discuss reunions of families separated by the 1950-53 Korean War.
The rapid rise in water levels along the Imjin river on 6 September occurred after the North abruptly released a massive amount of water from an upriver dam.
No advance warning was given of the release, which sent a surge of water across the heavily-fortified border between the two Koreas.
Shortly afterwards North Korea said it "urgently" had to open sluice gates because levels behind a dam on the river had become dangerously high.
The release caused the water levels in the river to almost double in a matter of minutes, sweeping to their deaths six South Koreans who were camping downstream and casting a cloud over recent improvements in inter-Korean relations.
North and South Korea remain technically at war, never having signed a peace treaty formally ending the 1950-53 Korean War.
The two sides last held formal talks in August, during which they agreed to resume a stalled programme of family reunions.