You may perhaps have heard of the flood we had here in Bavaria the last 2 weeks - my town was hit worst as a dam broke. Catastrophy Alert (that's basically like a national emergency of the highest level, only it's issued locally) was lifted only yesterday. There are no definite figures yet but the damage in my town alone is estimated to be around 0.8 billion Dollars.
My heart goes out to you. In 2011, in my home county in upstate NY, the entire valley flooded just as harvest season was in full swing. It was heartbreaking.
However, testing done following the floods indicated that the valley (once called "the Breadbasket of the American Revolution" because its fertility provided much of the food eaten by the colonial troops) fared pretty well, all things considered. Because the ground was saturated by heavy rains before Irene moved in, the toxic water simply rushed over the land & didn't settle. That year's harvest was lost, but there was no long term contamination.
Farmers further upstream on higher (and rockier) ground, however, had serious topsoil loss (one potato farmer lost 10 ft of topsoil) and some just gave up.
Your farmers are going to have to have their soil tested. I would assume (although maybe I shouldn't?) that you have an agricultural ministry or other bureaucracy that can give advice? Here in the US we have the state Cooperative Extensions (which is, at least in NY, based at the agricultural college).
I would give the same advice to gardeners: get your soil tested. You have to know what you're dealing with before you can do something about it.
ETA: The soil testing project in the Schoharie Valley was instigated by the high school agricultural sciences class--and in the end they won $100K in technology for their tiny rural school for the work they did.