MSF's Head of Mission in Chad, Audrey van der Schoot, said the flooding that usually occurs during this time of year could isolate refugees and host communities in Chad's eastern Sila region and other areas that share a border with Sudan.
"We fear that with the coming rainfall, people in this border area will be trapped and forgotten," she said, noting that arrivals from Sudan were continuing.
Rains will also bring a higher risk of waterborne and infectious diseases given poor access to clean water and sanitation, she said.
More than 100,000 people have fled across the border to Chad since conflict broke out in Sudan in April, and numbers could double over the next three months, the United Nations' refugee agency (UNHCR) warned earlier this month.
Nearly 30,000 refugees are in Sila, where they lack shelter, water and food due to deficiencies in humanitarian assistance. Many have moved in with local host families as a result, putting pressure on meagre resources, MSF said.
One of the poorest countries in the world, Chad was already hosting close to 600,000 refugees before the latest Sudanese crisis.
The UNHCR says Chad needs $214.1 million to provide vital services to displaced people in the Central African country, of which only 16% were funded at the start of June.
The conflict in Sudan is affecting Chadian citizens too, as those living near the border are no longer able to access healthcare and markets in Sudan. This has caused food and commodity prices to soar in areas already suffering from high levels of malnutrition, MSF said.