For those who have actually had a chance to put in early cool-season crops, the issue of food safety from the garden is best handled with caution. Clearly, if floodwaters are contaminated with raw sewage, it is risky to eat the produce. Crops that can be washed thoroughly, peeled and/or boiled should pose minimal risks. However, crops that are eaten uncooked, especially leafy crops such as spinach and lettuce, will be more risky for consumption since it is so difficult to remove all of the contamination with just plain rinsing.
Newly planted seeds and transplants may not survive even short-term flooding, and seeds may have washed away. Resist the urge to replant immediately; give the soil a chance to dry out first. Working wet soil will have long-lasting effects of soil compaction.
As for landscape trees and shrubs, it is difficult to say what the long-term effect of being underwater will be. When soils are completely flooded, oxygen is prevented from reaching the root system. Certainly, some trees are more tolerant of waterlogged conditions, but the longer the lack of aeration, the greater the chance of root death. The general thought is that most landscape plants can survive being submerged for about a week or so. However, extended lack of aeration to the roots will result in root die-back, with the above-ground symptoms appearing as leaf yellowing, droopy foliage, leaf drop and, eventually, branch die-back. Waterlogged root systems are also more susceptible to attack by root-rot organisms. In areas of severe flooding, concerns for plant health also include soil erosion and deposits of additional soil and silt. Both can damage the root system.
In addition to the obvious damage to plants, there are more long-term effects to soils, which have been flooded for extended periods. Soil microorganisms that require oxygen may be killed and those that survive without oxygen take over, which in turn affects availability of nutrients for plant use. The soil structure itself may be physically harmed due to compaction of soil particles.
There isn't much you can do other than wait for drier weather to prevail and allow water to drain. As more favorable conditions return, watch for signs of die-back, but don't be too hasty to cut limbs. Branches that have lost leaves aren't necessarily dead; even though leaves may drop, there may be buds that will be able to re-leaf yet this summer. Live stems and buds will have some green tissue visible. Remove only those limbs that are physically damaged or obviously dead. A light fertilization may be helpful to replace nutrients that were lost and to encourage re-growth.
We may not know the full effect of flooding until long after the water recedes. And then, of course, a lot will depend on what future stresses the weather may bring upon our landscapes.