The development agency fears one of the harshest winters in years may be just around the corner.
Countries neighbouring Syria are struggling to cope with a seven-fold increase in the number of refugees arriving in the last year as a result of the ongoing conflict.
Camps run by the United Nations are full and those forced into temporary shelters are at particular risk, Christian Aid warns.
In northern Iraq, where around 200,000 refugees have sought shelter, the winters often bring heavy rain and sometimes snow.
Christian Aid said most of the refugees were arriving with little or no belongings, and were ill-equipped to deal with the near freezing temperatures.
Its has provided financial support to partner organisation, REACH, which is working with refugees outside the official UN camps in Iraq.
REACH has so far distributed blankets, materials for shelter, warm clothes, food, sanitary products, and jerry cans for water to around 15,000 people.
However, REACH Director Saman Majed said refugees were already suffering malnutrition and diarrhoea, and health issues were expected to "escalate".
"The temporary camps were set up quickly to accommodate the last huge influx of 50,000 refugees in the summer and were not constructed to deal with harsh winter conditions," he said.
"Without proper drainage and concrete flooring in the tents the rainy winter season threatens hundreds of lives as tents will flood. A wet environment then increases the risk of disease, especially amongst small children and the elderly.
"Also at severe risk are the urban refugees those who have sought shelter in abandoned buildings with no doors or windows. They cannot afford clothes or fuel to burn to keep them warm."
In the coming weeks, REACH will be distributing kerosene heaters and oil, mattresses and blankets provided by German Aid agency Diakonie Katastrophenhilfe (DKH Germany).
In Lebanon, more than a million refugees are staying in makeshift encampments as there are no formal camps.
Christian Aid partner Najdeh is continuing to provide food and hygiene kits and with the help of Swiss International Church Aid (HEKS), will be providing heating and heating vouchers
Janet Symes, Head of Middle East at Christian Aid said: "Winter will soon arrive and this underlines the need to find a solution to the humanitarian crisis in Syria. Christian Aid believes the only way to end the crisis is through an inclusive negotiated peace that gives the Syrian people the opportunity to start rebuilding their future."