It has been raining since 20 October, and almost the whole country - 17 out of 18 provinces - is affected.
However, thanks to well-organised evacuations, the death toll is relatively low, with 41 people known to have died.
Christian Aid's local partners CASM, OCDIH, ASONOG and ACT Honduras are distributing food aid, bottled water, mattresses, blankets, cooking pots and hygiene kits to hundreds of families in temporary shelters.
The Reyes family has been homeless for three weeks.
The Reyes Nufio family, pictured, has been camped out on the roadside for three weeks - with seven people sharing one small tent.
As well as providing immediate relief supplies, partners will help repair wells, water pipes and toilets, and provide seeds, tools and organic fertiliser so that farmers can plant again.
Kick-starting agricultural production is vital because almost 50% of this year's crops have been lost, and the country will face serious food shortages in the months ahead.
Over the next few weeks Christian Aid partners are hoping to reach almost 28,000 people in the worst-affected areas.
'This is the worst flooding Honduras has experienced since Hurricane Mitch ten years ago,' explains Christian Aid's emergencies officer for Central America, Erwin Garzona.
'The impact is worse than Hurricane Felix in 2007 or Hurricane Bertha in 2004, but there has been little media coverage, partly because this situation is caused by continuous heavy rainfall rather than a dramatic hurricane strike.'
Christian Aid has been funding disaster risk reduction work in Honduras for several years, helping communities prepare for the annual storms, floods and landslides.
This has included helping villages set up early-warning systems, evacuation procedures and emergency shelter plans.
Partners have also helped communities build sturdy, high-level bridges, watertight metal granaries to store food safely and raised chicken coops to keep hens safe from floodwaters.