About 2,000 people are known to have died or disappeared and emergency teams are trying to recover bodies before they contaminate the water supply.
On Saturday an earthquake struck the border area between the two countries, compounding problems.
The quake was reported at a magnitude of 4.4.
Continuing rain is making matters worse in both countries.
In Haiti, relief agencies flew helicopters carrying food, water and medicines to submerged villages.
Among these is the Haitian village of Mapou, to the south-east of the capital Port-au-Prince.
Thousands of people who once lived there have sought refuge on high ground, where food and clean water are being handed out.
Relief co-ordinator Guy Gauvreau, of the World Food Programme, said: “We are extremely worried by the fact that we are limited in our logistics because we are unable to reach the place with our trucks.”
US-led peacekeeping troops – who were sent to Haiti after the overthrow of President Jean-Bertrand Aristide in February – have been taking part in the relief effort.
In the Dominican Republic, the affected area is expected to be sprayed from the air with disinfectant.
The border town of Jimani suffered the worst casualties, with 329 bodies found and at least 300 people are missing.
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Floodwaters which had been beginning to drain from the worst-affected areas look set to rise again.
The BBC’s Stephen Gibbs in Port-au-Prince says that as every day passes, the threat of disease increases.
Recovery teams are using boats to search for bodies before they contaminate the water supply.
Doctors say they also may have to move dozens of corpses that have been buried in mass graves that were too shallow.