Now, as the waters are receding and the mopping up gets under way, the farming communities in south and east Germany, Slovakia, Austria, Czech Republic, Serbia, Hungary, Switzerland and Poland are starting to count the cost of the damage.
While the initial destruction of towns, farms and agricultural land will be immediately apparent, the cost in losses of livestock and the potential loss of crops and the harvest in these regions and the knock on effect have still to be established.
The worst of the devastation is along the banks of the Rivers Danube and Elbe and their tributaries.
In the Czech Republic, 10 people are reported dead and although last week the European Commission reported that the water levels are decreasing and flood containment, pumping and clean-up are on-going, the devastation is vast.
The Czech minister of agriculture Petr Bendl has estimated the cost of the damage to the agricultural sector at 3.3 billion crowns (more than €128 million).
"We will activate the so-called dormant programmes that the Ministry of Agriculture has. These programmes are designed only in the event of floods, so that we are able to help financially, where flooding has damaged the water supply and sewerage or property on the Vltava and Elbe," said Minister Bendl.
"To help farmers more, we propose that where farmers are affected by floods they should delay their payments to the state. We are also giving them the opportunity to get a loan at the lowest possible interest rate."
"The current level of damage in the agricultural sector is 3.3 billion crowns although the exact amount cannot be quantified until all the water subsides.
“The damage to agricultural production has been estimated at 1 billion crowns, but again, the full amount has not yet estimated by the water managers. Most affected by the floods were fishermen and vegetable growers," said Minister Bendl.
The Trebon Fishery saw140-150 ponds damaged. The Rosenberg pond fulfilled its role, thanks to its unique retention capabilities to protect the environment from greater damage. Fishermen lost carp fingerlings and fish shaft, which will hit the fish farms for at least two years. Total damage in the fishing industry will not be known until the autumn after harvesting the ponds.
"I want to assure farmers that the State Agricultural Intervention Fund has people on the ground, who are assessing the damage. Since the beginning of June the website of the Ministry of Agriculture has been giving methodical information on the damage caused by floods," said First Deputy Minister William Zak.
The Czech Republic has accepted assistance from Poland, Germany and Slovakia.
In Germany, three people have lost their lives. The flooding situation is slowly improving along the Danube but is still critical on the Elbe.
In Saxony-Anhalt many dikes are flooded, some are broken and evacuations are taking place.
The State Secretary of the BMELV Dr Robert Kloos said that the full extent of the damage in the flood region of Germany was not yet known.
“We know that a large area flooded agricultural and forestry land and crops were destroyed, and many other assets have been damaged.
“We assume that the damage is going to be in the mid hundreds of millions range in the agricultural sector alone."
Dr Kloos said that emergency aid now had to be made available quickly, including federal aid and aid to the inland fisheries and aquaculture as well as to agriculture.
Germany has accepted assistance from Belgium, Denmark, Luxembourg and the Netherlands.
In Hungary, protection works are continuing in critical areas, but the flooding is now moving downstream from Budapest.
The prime minister, Viktor Orbán, said that unprecedented collaboration had helped to mitigate the impact of the floods.
And he said that EU assistance in compensation could not be ruled out.
In Austria, there have been five victims and two people are reported missing. Clean-up is on-going in the flooded areas, but the risk of landslides remains.
Agriculture Minister Berlakovich said: "We are currently reviewing all the ways we can help the farmers quickly and efficiently. The aim is clearly to safeguard the lives of those affected and to support them as much as possible. In a first step, the challenge now is to carry out an accurate assessment of damage. Then we can take immediate efforts in the way of relief. "
In Slovakia, the situation around Bratislava is stable. Despite record water level of the Danube, flood-countering measures have helped prevent major damage, according to the European Commission.
In Serbia, water levels are reportedly rising. Protection activities are taking place.
In Poland, more than 100,000 farms and 600,000 hectares of agricultural land has been affected by the floods.
The minister of Agriculture Stanislaw Kalemba said that his ministry has prepared an assistance programme that is to be submitted to the council of ministers and could be in operation by 15 July.
The assistance will include low interest rate loans, delaying, staggering or even cancelling payments due to ASIF and other agricultural bodies.
He said that aid would be made available for those who have lost more than 30 per cent of their agricultural production and this is expected to benefit at least 6,000 farmers so far. Other aid measures are also to be put in place.
Across Europe, the Emergency Response Centre (ERC) is monitoring developments and is in constant contact with the authorities in the affected countries.
So far, there has been no request for assistance through the EU Civil Protection Mechanism, but satellite images of the flooding evolution have been provided through the ERC.
The EU Civil Protection Mechanism, managed through the ERC, has at its disposal 30 flood-related response modules, registered by 11 countries.
*Picture courtesy of the European Commission