Under future climate predictions, the incidence of coastal flooding is set to rise. Many coastal regions at risk, such as those surrounding the North Sea, comprise large areas of low-lying and productive agricultural land. Flood risk assessments typically emphasise the economic consequences of coastal flooding on urban areas and national infrastructure. Impacts on agricultural land have seen less attention, and considerations tend to omit the long-term effects of soil salinity. The aim of this study is to develop a universal framework to evaluate the economic impact of coastal flooding to agriculture. We incorporated existing flood models, satellite acquired crop data, soil salinity, and crop sensitivity to give a novel and detailed assessment of salt damage to agricultural productivity over time. We focussed our case-study on low-lying, highly productive agricultural land with a history of flooding in Lincolnshire, UK. The potential impact of agricultural flood damage varied across our study region. Assuming typical cropping does not change postflood financial losses range from £1,366/ha to £5,526/ha per inundation, these losses would be reduced by between 35% up to 85% in the likely event that an alternative, more salt-tolerant, cropping, regime is implemented postflood. These losses are substantially higher than loses calculated on the same areas using established flood risk assessment framework conventionally used for freshwater flood assessments, with differences attributed to our longer term salt damage projections impacting over several years. This suggests flood protection policy needs to consider local and long-term impacts of flooding on agricultural land.