With excess water the life threatening damage to the plant is not from nutrient uptake sites being blocked, nor from the plant taking in too much water.

Super-saturated soil holds so little oxygen the roots & garden microbes use it up quickly. These microbes fight to survive by taking electrons from where ever found & the tips of the roots are affected.

But, when the root tips don't have enough oxygen to keep the unique part inside their cells where ATP energy is processed, the mitochondria, then it is a matter of hours until (root) die back occurs.

Lowest oxygen levels in the root zone is a state that means a 15 fold decrease in vital ATP production. The root cell's interior fluid's pH goes awry, swings acidic & then cell's encompassing membrane is degraded (which means functional failures arise).

Not all tomatoes respond the same to excess water. Poster of July 6,09 "EarthTainers w/Yellow -leaved Tomatoes" noted the hybrid Early Girl was comparatively unaffected.

The mechanics of surviving insufficient soil oxygen is to generate the ATP energy needed by fermenting the root storage starch, an anaerobic pathway.

With enough ATP the cells get to live & overcome water logging problem.

The genetic breeding that confers resistance to root pathogens gives some hybrid varieties (ex. Early Girl) the enhanced ability to power themselves up with alternate ATP, even though membrane under challenge from outside. The root pathogen is still in the soil; but inside, these (tomato) root cell's, it's mitochondria have called on back up ATP power source. These roots can then keep functioning while the root pathogen attack is blunted as it spends it's (the pathogens) force.

Excess water does more damage as the carbon dioxide (CO2) byproducts of root activity can not get away, nor can ethylene gas. These damage the roots & limit the roots' ability to move on along toward oxygen.

With flooded soil the anaerobic bacteria come to life. As a consequence of their metabolism of trace minerals, there are enzymes put into overdrive that also adversely affect root membranes.

Yellow leaves are a sign that Nitrogen (N) is missing. The same anaerobic bacteria act to make N into a form that the plant simply can not use. A readily assimilable form of N fertilization is good for plant recovery. There is leaching of nutrients from excess water, but the yellow leaf is not always indicating that N is gone from the soil.

As for the notable tomato leaf droop downward (epinasty) in wet conditions. It is the leaf's top side cells extra expanding that creates a shape with less surface for photons to hit. This slows the rate of photosynthesis because oxygen deprived plant's roots can not cope with a normal load of metabolism.

Epinasty also includes the leaf stoma shutting, as a protective mechanism to retain water inside the plant, since counter-intuitively the plant is not able to take up water in super-saturated conditions.

It (epinasty) is part of a hormone surge that is driven by enzymes activated about 1 hour into flooded conditions. The chain reaction ensures a ethylene hormone surge about 6 hours along that guides the leaf to protective droop.

Veteran posters tell us the droop is something the plant recovers from.

Ethylene is also involved in pre-programed (genetic) cell functions a plant will go through. Cell death progression is one genetic process; in other words some things die in order for other cells to survive. Root tips are OK to sacrifice if enough regenerative sites can be preserved; ditto leaves.

As for super-saturated soil, if the ethylene concentration stays hyper elevated there is definitely the possibility of root death in as little as 2 days. Some hobby growers are amazed how a healthy plant can die so quickly; it is not from lack of nutrients (which is a slow decline). Even open field commercial growers have spots where tomato plant suffer from excess water. Flood & drain hydroponics sounds risky, but the aeration phase is the plant savior.

My linking skills keep me from suggesting other posters' instructions on progression of growing medium collapse, 'Tainer substrate selection, fast draining container theories & different in ground soil characteristics. Any poster's chiming in are also invited to link input, as GW's search function confuses many of us.