The estimate is based on projections of climate change, land subsidence and urban growth in coastal centres. Three US cities -Miami, New York and New Orleans - and Guangzhou in China are expected to shoulder 43% of the burden.
The researchers based their predictions on data from 136 of the largest coastal urban settlements.
They found that socio-economic changes alone were likely to raise the cost of flood damage from £4bn in 2005 to £33bn in 2050.
Adding the effects of climate change and subsidence brought total losses to an "unacceptable" one trillion dollars.
The scientists, led by Stephane Hallegatte from the World Bank in Washington DC, said: "There is a need to prepare at the local, national and international level for larger floods."